From 996dcdf06438db48bc65112c619dbb8cee423793 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tor=20Bj=C3=B6rgen?= Date: Mon, 8 Dec 2025 15:13:43 +0100 Subject: [PATCH 1/2] VRS: Change VCF inference key from VrsModel.* to Mivmir.* MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Tor Björgen --- src/rdds/gicam/__main__.py | 2 +- src/rdds/gicam/model/model.py | 2 +- src/rdds/gicam/vcf_inference/infer_vcf.py | 4 +- .../explore_patient_cases.ipynb | 50 +++++++++---------- .../view_vcf_rank_results.py | 8 +-- .../vcf_inference/predict_on_vcf.py | 14 +++--- src/tests/gicam/inference_test_data.vcf | 10 ++-- src/tests/gicam/test_inference.py | 2 +- .../test_data-predictions-ref.vcf | 30 +++++------ .../variant_rank_score/test_inference.py | 17 +++---- 10 files changed, 69 insertions(+), 70 deletions(-) diff --git a/src/rdds/gicam/__main__.py b/src/rdds/gicam/__main__.py index eb81dc25..03ecdc46 100644 --- a/src/rdds/gicam/__main__.py +++ b/src/rdds/gicam/__main__.py @@ -79,7 +79,7 @@ def _explore(args): help='Number of CPU cores to allocate for processing', default=cpu_count() - 1) subparser.add_argument('--replace_overwrite_vrs', - help='Write GICAM inference value to VrsModelPrediction field instead of separate GICAM' + + help='Write GICAM inference value to MivmirScore field instead of separate GICAM' + '(not to be used in production)', default=False) def _infer_vcf(args): diff --git a/src/rdds/gicam/model/model.py b/src/rdds/gicam/model/model.py index 88fbadb6..ede9a01c 100644 --- a/src/rdds/gicam/model/model.py +++ b/src/rdds/gicam/model/model.py @@ -468,7 +468,7 @@ def score_variants(self, variants: List[Variant]) -> np.ndarray: score_mivmir: np.ndarray = np.zeros((n_samples, 1)) # [batch_dim, feature_dim] score_genmod: np.ndarray = np.zeros((n_samples, 1)) for i, variant in enumerate(variants): - score_mivmir[i, 0] = variant.INFO['VrsModelPrediction'] + score_mivmir[i, 0] = variant.INFO['MivmirScore'] rank_score_normalized_str: str = variant.INFO['RankScoreNormalized'] # format: str: case_name:rank_score rank_score = float(rank_score_normalized_str.split(':')[1]) score_genmod[i, 0] = rank_score diff --git a/src/rdds/gicam/vcf_inference/infer_vcf.py b/src/rdds/gicam/vcf_inference/infer_vcf.py index d364ef37..de40c76d 100644 --- a/src/rdds/gicam/vcf_inference/infer_vcf.py +++ b/src/rdds/gicam/vcf_inference/infer_vcf.py @@ -34,7 +34,7 @@ def _infer_gicam_fn(vcf_file_path: str, # Make a copy of the input VCF which is also the output file subprocess_output_file_name = os.path.join(subprocess_work_dir, f'{variant_index_start}.vcf') vcf_writer = VcfWriter(subprocess_output_file_name, - vcf_reader, # Reuse original file header, with VrsModelPrediction appended + vcf_reader, # Reuse original file header, with MivmirScore appended mode='w') # Load and preprocess variants # Force load complete VCF into RAM as list of variants, drop out of scope variants @@ -47,7 +47,7 @@ def _infer_gicam_fn(vcf_file_path: str, scores = gicam.score_variants(variants=variants) for i, (variant, score) in enumerate(zip(variants, scores)): if replace_overwrite_vrs_annotation: - variant.INFO['VrsModelPrediction'] = f'{score:.5f}' + variant.INFO['MivmirScore'] = f'{score:.5f}' else: variant.INFO['GICAM'] = f'{score:.5f}' vcf_writer.write_record(variant) diff --git a/src/rdds/variant_rank_score/inference_exploration/explore_patient_cases.ipynb b/src/rdds/variant_rank_score/inference_exploration/explore_patient_cases.ipynb index df8b3e7c..8dbc6162 100644 --- a/src/rdds/variant_rank_score/inference_exploration/explore_patient_cases.ipynb +++ b/src/rdds/variant_rank_score/inference_exploration/explore_patient_cases.ipynb @@ -209,9 +209,9 @@ "def visualize_numerical_feature_vs_rank_score(df, annotation):\n", " fig = plt.figure(figsize=FIGSIZE)\n", " ax = fig.add_subplot()\n", - " sb.scatterplot(df[[annotation, 'VrsModelPrediction']],\n", + " sb.scatterplot(df[[annotation, 'MivmirScore']],\n", " x=annotation,\n", - " y='VrsModelPrediction',\n", + " y='MivmirScore',\n", " ax=ax)\n", " fig.tight_layout()\n", " fig.suptitle(f'n={len(df[annotation].dropna())} ({len(df)})')\n", @@ -269,7 +269,7 @@ " data = df[[annotation]]\n", " for index, row in data.iterrows():\n", " sentence = _preprocess_text(row[annotation])\n", - " _preprocessed_df = pd.DataFrame(data={'VrsModelPrediction': df.loc[index].VrsModelPrediction,\n", + " _preprocessed_df = pd.DataFrame(data={'MivmirScore': df.loc[index].MivmirScore,\n", " annotation: sentence,\n", " 'case_name': df.loc[index].case_name},\n", " index=[index])\n", @@ -277,7 +277,7 @@ " preprocessed_df = _preprocessed_df\n", " else: \n", " preprocessed_df = pd.concat((preprocessed_df, _preprocessed_df), axis=0)\n", - " facet = sb.relplot(data=preprocessed_df, x='case_name', y='VrsModelPrediction', hue=annotation, style=annotation, kind='scatter', height=FIGSIZE[1],\n", + " facet = sb.relplot(data=preprocessed_df, x='case_name', y='MivmirScore', hue=annotation, style=annotation, kind='scatter', height=FIGSIZE[1],\n", " aspect = FIGSIZE[0] / FIGSIZE[1])\n", " facet.set(xticklabels=[])\n", " facet.set(title=f'n={len(preprocessed_df.dropna())} ({len(df)})')\n", @@ -292,13 +292,13 @@ "outputs": [], "source": [ "def print_nan_entries(df, annotation):\n", - " nan_entries = df.loc[df[annotation].isna()][['VrsModelPrediction', annotation]]\n", + " nan_entries = df.loc[df[annotation].isna()][['MivmirScore', annotation]]\n", " if len(nan_entries) > 0:\n", " print(nan_entries, flush=True)\n", - " mean = nan_entries.VrsModelPrediction.mean()\n", - " std = nan_entries.VrsModelPrediction.std()\n", + " mean = nan_entries.MivmirScore.mean()\n", + " std = nan_entries.MivmirScore.std()\n", " print(f'mean {mean:.4f} std {std:.4f}')\n", - " return nan_entries.VrsModelPrediction" + " return nan_entries.MivmirScore" ] }, { @@ -316,8 +316,8 @@ " 'Compounds_family_id',\n", " 'CompoundsNormalized',\n", " 'CSQ_ENSP',\n", - " 'VrsModelExplanation',\n", - " 'VrsModelPrediction']\n", + " 'MivmirExplanation',\n", + " 'MivmirScore']\n", "\n", "annotation_nan_statistics = {} # Keep track of pathogenicity scores for empty annotations\n", "\n", @@ -357,9 +357,9 @@ " if d < 0.2 : # if bias are less than\n", " continue\n", " facet = sb.displot(data=nan_scores, kind='hist', binwidth=0.1)\n", - " facet.set_xlabels('VrsModelPrediction Score')\n", + " facet.set_xlabels('MivmirScore Score')\n", " facet.set(xlim=(-0.1, 1.1))\n", - " facet.set(title=f'VrsModelPrediction\\non {annotation} NaNs n={len(nan_scores)}')\n", + " facet.set(title=f'MivmirScore\\non {annotation} NaNs n={len(nan_scores)}')\n", " facet.tight_layout()" ] }, @@ -411,11 +411,11 @@ " df_annotation_info = _df_annotation_info\n", " else:\n", " df_annotation_info = pd.concat((df_annotation_info, _df_annotation_info), axis=1)\n", - "df_annotation_info['VrsModelPrediction'] = df.VrsModelPrediction\n", + "df_annotation_info['MivmirScore'] = df.MivmirScore\n", "df_annotation_info['case_name'] = df.case_name\n", "\n", "for annotation in annotations:\n", - " facet = sb.relplot(data=df_annotation_info, x=f'{annotation}%', y='VrsModelPrediction', kind='scatter', height=FIGSIZE[1],\n", + " facet = sb.relplot(data=df_annotation_info, x=f'{annotation}%', y='MivmirScore', kind='scatter', height=FIGSIZE[1],\n", " aspect = FIGSIZE[0] / FIGSIZE[1])\n", " facet.set(title=f'Annotation magnitude {annotation}')\n", " facet.tight_layout()" @@ -429,14 +429,14 @@ "outputs": [], "source": [ "annotation_magnitudes = df_annotation_info.iloc[:, :-5].sum(axis=1)\n", - "facet = sb.relplot(x=annotation_magnitudes, y=df_annotation_info.VrsModelPrediction, hue=df_annotation_info.case_name, style=df_annotation_info.case_name, kind='scatter', height=FIGSIZE[1],\n", + "facet = sb.relplot(x=annotation_magnitudes, y=df_annotation_info.MivmirScore, hue=df_annotation_info.case_name, style=df_annotation_info.case_name, kind='scatter', height=FIGSIZE[1],\n", " aspect = FIGSIZE[0] / FIGSIZE[1])\n", "for index, row in df_annotation_info.iterrows():\n", - " facet.ax.text(annotation_magnitudes.loc[index], row.VrsModelPrediction, row.case_name, fontsize=6, rotation=40)\n", + " facet.ax.text(annotation_magnitudes.loc[index], row.MivmirScore, row.case_name, fontsize=6, rotation=40)\n", "facet.set(xlabel='Total Annotation Magnitude')\n", "facet.set(title=f'Overall annotation magnitude')\n", "facet.tight_layout()\n", - "pd.concat((annotation_magnitudes, df_annotation_info[['case_name', 'VrsModelPrediction']]), axis=1).sort_values(0)" + "pd.concat((annotation_magnitudes, df_annotation_info[['case_name', 'MivmirScore']]), axis=1).sort_values(0)" ] }, { @@ -450,13 +450,13 @@ "df_investigate_framshift_missense = pd.DataFrame()\n", "df_investigate_framshift_missense['consequence'] = df.CSQ_Consequence\n", "df_investigate_framshift_missense['annotation_magnitude'] = annotation_magnitudes\n", - "df_investigate_framshift_missense['VrsModelPrediction'] = df.VrsModelPrediction\n", + "df_investigate_framshift_missense['MivmirScore'] = df.MivmirScore\n", "df_investigate_framshift_missense['case_name'] = df.case_name\n", "df_investigate_framshift_missense.sort_values('consequence', inplace=True)\n", "\n", "facet = sb.relplot(y=df_investigate_framshift_missense.consequence,\n", " x=df_investigate_framshift_missense.annotation_magnitude,\n", - " hue=df_investigate_framshift_missense.VrsModelPrediction,\n", + " hue=df_investigate_framshift_missense.MivmirScore,\n", " height=FIGSIZE[1],\n", " aspect=FIGSIZE[0] / FIGSIZE[1])\n", "for index, row in df_investigate_framshift_missense.iterrows():\n", @@ -626,7 +626,7 @@ "metadata": {}, "outputs": [], "source": [ - "points = df[['VrsModelPrediction','case_name']]\n", + "points = df[['MivmirScore','case_name']]\n", "points" ] }, @@ -671,7 +671,7 @@ "num_plot = cosmo(\n", " points = points,\n", " point_label_by = 'case_name',\n", - " point_color_by = 'VrsModelPrediction',\n", + " point_color_by = 'MivmirScore',\n", " links = links_numerical,\n", " link_source_by = 'sources',\n", " link_target_by = 'targets',\n", @@ -780,7 +780,7 @@ "txt_plot = cosmo(\n", " points = points,\n", " point_label_by = 'case_name',\n", - " point_color_by = 'VrsModelPrediction',\n", + " point_color_by = 'MivmirScore',\n", " links = links_text,\n", " link_source_by = 'sources',\n", " link_target_by = 'targets',\n", @@ -835,7 +835,7 @@ "num_text_plot = cosmo(\n", " points = points,\n", " point_label_by = 'case_name',\n", - " point_color_by = 'VrsModelPrediction',\n", + " point_color_by = 'MivmirScore',\n", " links = links_numerical_text,\n", " link_source_by = 'sources',\n", " link_target_by = 'targets',\n", @@ -871,14 +871,14 @@ "outputs": [], "source": [ "facet = sb.relplot(x=df.case_name,\n", - " y=df.VrsModelPrediction,\n", + " y=df.MivmirScore,\n", " hue=df.case_name,\n", " style=df.case_name,\n", " height=FIGSIZE[1],\n", " aspect = FIGSIZE[0] / FIGSIZE[1],\n", " palette='rocket')\n", "for index, row in df.iterrows():\n", - " facet.ax.text(row.case_name, row.VrsModelPrediction, row.case_name, fontsize=6, rotation=40)\n", + " facet.ax.text(row.case_name, row.MivmirScore, row.case_name, fontsize=6, rotation=40)\n", "facet.set(xticklabels=[])" ] }, diff --git a/src/rdds/variant_rank_score/inference_exploration/view_vcf_rank_results.py b/src/rdds/variant_rank_score/inference_exploration/view_vcf_rank_results.py index 5162b348..eff1e7c9 100644 --- a/src/rdds/variant_rank_score/inference_exploration/view_vcf_rank_results.py +++ b/src/rdds/variant_rank_score/inference_exploration/view_vcf_rank_results.py @@ -73,7 +73,7 @@ def view_vcf_rank_results(vcf_file_path: str, vrs_rank_score = np.empty(n_variants) frq = np.empty(n_variants) vrs_model_explanation = np.empty(n_variants, dtype=object) - parse_only_fields = ['POS', 'CHROM', 'RankScore', 'RankScoreNormalized', 'VrsModelPrediction', 'Frq'] + parse_only_fields = ['POS', 'CHROM', 'RankScore', 'RankScoreNormalized', 'MivmirScore', 'Frq'] pbar = ProgressBar(max_value=n_variants) _LOGGER.info(f'{vcf_file_path}, n={n_variants} variants') for i, variant in enumerate(variants): @@ -97,12 +97,12 @@ def view_vcf_rank_results(vcf_file_path: str, genmod_rank_score_normalized[i] = parsed_variant.RankScoreNormalized_value else: genmod_rank_score_normalized[i] = np.nan - if 'VrsModelPrediction' in parsed_variant.parsed_fields: - vrs_rank_score[i] = parsed_variant.VrsModelPrediction + if 'MivmirScore' in parsed_variant.parsed_fields: + vrs_rank_score[i] = parsed_variant.MivmirScore else: vrs_rank_score[i] = np.nan try: - vrs_model_explanation[i] = variant.INFO['VrsModelExplanation'] + vrs_model_explanation[i] = variant.INFO['MivmirExplanation'] except KeyError: pass pbar.update(i) diff --git a/src/rdds/variant_rank_score/vcf_inference/predict_on_vcf.py b/src/rdds/variant_rank_score/vcf_inference/predict_on_vcf.py index 2e35f107..18e0f0ef 100644 --- a/src/rdds/variant_rank_score/vcf_inference/predict_on_vcf.py +++ b/src/rdds/variant_rank_score/vcf_inference/predict_on_vcf.py @@ -20,19 +20,19 @@ def _subprocess_predict_on_vcf_part(vcf_file_path: str, variant_index_stop: int): from ..model import VariantRankScoreModel vcf_reader = VCFReader(vcf_file_path) - vcf_reader.add_info_to_header({'ID': 'VrsModelPrediction', - 'Description': 'Rank score from VRS model (5 points precision)', + vcf_reader.add_info_to_header({'ID': 'MivmirScore', + 'Description': 'Rank score from MIVMIR model (5 points precision)', 'Type': 'Float', 'Number': '1'}) - vcf_reader.add_info_to_header({'ID': 'VrsModelExplanation', - 'Description': 'List of annotation impact scores on VrsModelPrediction (2 points precision)', + vcf_reader.add_info_to_header({'ID': 'MivmirExplanation', + 'Description': 'List of annotation impact scores on MivmirScore (2 points precision)', 'Type': 'String', 'Number': '.'}) # Make a copy of the input VCF which is also the output file subprocess_output_file_name = os.path.join(subprocess_work_dir, f'{variant_index_start}.vcf') vcf_writer = VcfWriter(subprocess_output_file_name, - vcf_reader, # Reuse original file header, with VrsModelPrediction appended + vcf_reader, # Reuse original file header, with MivmirScore appended mode='w') # Load and preprocess variants @@ -55,7 +55,7 @@ def _subprocess_predict_on_vcf_part(vcf_file_path: str, df: pd.DataFrame = vrs_model.score_variant(parsed_variants) for i, variant in enumerate(variants): df_i = df.iloc[i] - variant.INFO['VrsModelPrediction'] = f'{df_i.pathogenicity_score:.5F}' + variant.INFO['MivmirScore'] = f'{df_i.pathogenicity_score:.5F}' # Sort the explanations in decreasing importance (positive = more contributing to higher scoring result) explanations_sorted_in_decreasing_importance = df_i.sort_values(ascending=False) vrs_model_explanations = '[' @@ -66,7 +66,7 @@ def _subprocess_predict_on_vcf_part(vcf_file_path: str, continue vrs_model_explanations += f'{key}={contribution_score:.2F},' vrs_model_explanations += ']' - variant.INFO['VrsModelExplanation'] = vrs_model_explanations + variant.INFO['MivmirExplanation'] = vrs_model_explanations vcf_writer.write_record(variant) vcf_writer.close() vcf_reader.close() diff --git a/src/tests/gicam/inference_test_data.vcf b/src/tests/gicam/inference_test_data.vcf index 224874b0..57810120 100644 --- a/src/tests/gicam/inference_test_data.vcf +++ b/src/tests/gicam/inference_test_data.vcf @@ -84,8 +84,8 @@ ##INFO= ##INFO= ##INFO= -##INFO= -##INFO= +##INFO= +##INFO= ##INFO= ##INFO= ##INFO= @@ -214,6 +214,6 @@ ##rs_dbSNP150=rs_dbSNP150 from dbNSFP file ##LoFtool=LoFtool score for gene #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLENAME -1 2 1_C_A C A 68 . VrsModelPrediction=0.98754;RankScore=casename:8.0;RankScoreNormalized=casename:1.0;RankScoreMinMax=casename:-29.0:8.0;RankResult=4|1|3 GT:DP:AD:GQ:PL:RNC 0/1:32:13,18:67:68,0,76:.. -1 3 1_3_AG_A AG A 40 . VrsModelPrediction=0.00123;RankScore=casename:6.0;RankScoreNormalized=casename:0.9459459459459459;RankScoreMinMax=casename:-29.0:8.0;RankResult=4|1|1 GT:DP:AD:GQ:PL:RNC 1/1:16:3,13:18:40,17,0:.. -1 4 1_4_C_G C G 49 . VrsModelPrediction=1.00000;RankScore=casename:8.0;RankScoreNormalized=casename:1.0;RankScoreMinMax=casename:-29.0:8.0;RankResult=4|1|3 GT:DP:AD:GQ:PL:RNC 0/1:12:5,7:49:49,0,60:.. +1 2 1_C_A C A 68 . MivmirScore=0.98754;RankScore=casename:8.0;RankScoreNormalized=casename:1.0;RankScoreMinMax=casename:-29.0:8.0;RankResult=4|1|3 GT:DP:AD:GQ:PL:RNC 0/1:32:13,18:67:68,0,76:.. +1 3 1_3_AG_A AG A 40 . MivmirScore=0.00123;RankScore=casename:6.0;RankScoreNormalized=casename:0.9459459459459459;RankScoreMinMax=casename:-29.0:8.0;RankResult=4|1|1 GT:DP:AD:GQ:PL:RNC 1/1:16:3,13:18:40,17,0:.. +1 4 1_4_C_G C G 49 . MivmirScore=1.00000;RankScore=casename:8.0;RankScoreNormalized=casename:1.0;RankScoreMinMax=casename:-29.0:8.0;RankResult=4|1|3 GT:DP:AD:GQ:PL:RNC 0/1:12:5,7:49:49,0,60:.. diff --git a/src/tests/gicam/test_inference.py b/src/tests/gicam/test_inference.py index e90b3a22..39e727b0 100644 --- a/src/tests/gicam/test_inference.py +++ b/src/tests/gicam/test_inference.py @@ -21,7 +21,7 @@ def test_vcf_inference(work_dir, overwrite_vrs_annotation): reader = VCFReader(output_file, 'r') target_annotation = 'GICAM' if overwrite_vrs_annotation: - target_annotation = 'VrsModelPrediction' + target_annotation = 'MivmirScore' assert target_annotation in reader.info_fields for variant in list(reader): assert isinstance(variant.INFO[target_annotation], float) diff --git a/src/tests/variant_rank_score/test_data-predictions-ref.vcf b/src/tests/variant_rank_score/test_data-predictions-ref.vcf index 2fc4626f..9eed296f 100644 --- a/src/tests/variant_rank_score/test_data-predictions-ref.vcf +++ b/src/tests/variant_rank_score/test_data-predictions-ref.vcf @@ -107,19 +107,19 @@ ##Software= ##bcftools_concatVersion=1.16+htslib-1.16 ##bcftools_concatCommand=concat -o /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/endvariantannotationblock/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.selected.vcf --output-type v /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.1_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.2_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.3_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.4_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.5_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.6_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.7_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.8_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.9_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.10_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.11_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.12_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.13_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.14_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.15_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.16_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.17_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.18_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.19_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.20_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.21_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.22_selected.vcf /home/tor.bjorgen/repos/cg/mip/cases/clinvar/analysis/clinvar/rankvariant/clinvar_vrn_norm_af_cadd_vep_parsed_ranked.X_selected.vcf; Date=Mon Aug 28 10:42:30 2023 -##INFO= -##INFO= +##INFO= +##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NOTASAMPLE -1 1336445 2052067 A T . . CSQ=T|downstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000344843|protein_coding|||||||||||843|-1||HGNC|14478|YES|||CCDS26.1|ENSP00000341082|RM20_HUMAN||UPI000006F0A8|||Ensembl||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||,T|downstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000482352|protein_coding|||||||||||4044|-1||HGNC|14478|||||ENSP00000460924||B7Z746_HUMAN|UPI00019151C3|||Ensembl||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||,T|downstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000487659|retained_intron|||||||||||848|-1||HGNC|14478|||||||||||Ensembl||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||,T|downstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000492508|protein_coding|||||||||||1117|-1|cds_start_NF|HGNC|14478|||||ENSP00000459994||I3L2X1_HUMAN|UPI00025A2C10|||Ensembl||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||,T|downstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000493287|processed_transcript|||||||||||848|-1||HGNC|14478|||||||||||Ensembl||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||,T|downstream_gene_variant|MODIFIER|MRPL20|55052|Transcript|NM_001318485.2|protein_coding|||||||||||844|-1||EntrezGene|14478|||||NP_001305414.1||||||RefSeq||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||,T|downstream_gene_variant|MODIFIER|MRPL20|55052|Transcript|NM_017971.4|protein_coding|||||||||||844|-1||EntrezGene|14478|YES||||NP_060441.2||||||RefSeq||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||;CLINVAR_GROUND_TRUTH=Likely_benign;CADD=3.648;most_severe_consequence=14478:T|downstream_gene_variant;Annotation=MRPL20;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;VrsModelPrediction=0.00013;VrsModelExplanation=[] GT:DP:AD:GQ 1/1:30:4,26:38 -1 976215 1320032 T G . . CSQ=G|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000379370|protein_coding|4/36||ENST00000379370.2:c.682T>G|ENSP00000368678.2:p.Cys228Gly|732|682|228|C/G|Tgc/Ggc|||1||HGNC|329|YES|||CCDS30551.1|ENSP00000368678|AGRIN_HUMAN|Q5XG79_HUMAN|UPI00001D7C8B|||Ensembl||T|T||deleterious|probably_damaging|Gene3D:3.30.60.30&Pfam:PF07648&PROSITE_profiles:PS51465&PANTHER:PTHR10574&PANTHER:PTHR10574:SF227&SMART:SM00057&SMART:SM00280&Superfamily:SSF100895|||||||3.6|3.6|0.67229|0.347|1.000000|3.561000||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|2.071|8.024|4.707|10.126|-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||,G|non_coding_transcript_exon_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000469403|retained_intron|2/3||ENST00000469403.1:n.629T>G||629|||||||1||HGNC|329|||||||||||Ensembl||T|T||||||||||||||||||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|2.071|8.024|4.707|10.126|-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||,G|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000477585|processed_transcript|||||||||||110|1||HGNC|329|||||||||||Ensembl||T|T||||||||||||||||||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|||||-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||,G|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000479707|retained_intron|||||||||||4564|1||HGNC|329|||||||||||Ensembl||T|T||||||||||||||||||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|||||-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||,G|missense_variant|MODERATE|AGRN|375790|Transcript|NM_001305275.2|protein_coding|4/39||NM_001305275.2:c.682T>G|NP_001292204.1:p.Cys228Gly|735|682|228|C/G|Tgc/Ggc|||1||EntrezGene|329|YES||||NP_001292204.1||||||RefSeq||T|T||deleterious|probably_damaging||||||||3.6|3.6|0.67229|0.347|1.000000|3.561000||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|2.071|8.024|4.707|10.126|-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||,G|missense_variant|MODERATE|AGRN|375790|Transcript|NM_001364727.2|protein_coding|3/36||NM_001364727.2:c.367T>G|NP_001351656.1:p.Cys123Gly|930|367|123|C/G|Tgc/Ggc|||1||EntrezGene|329|||||NP_001351656.1||||||RefSeq||T|T|||||||||||3.6|3.6|0.67229|0.347|1.000000|3.561000||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|2.071|8.024|4.707|10.126|-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||,G|missense_variant|MODERATE|AGRN|375790|Transcript|NM_198576.4|protein_coding|4/36||NM_198576.4:c.682T>G|NP_940978.2:p.Cys228Gly|735|682|228|C/G|Tgc/Ggc|||1||EntrezGene|329|||||NP_940978.2||||||RefSeq||T|T||deleterious|probably_damaging||||||||3.6|3.6|0.67229|0.347|1.000000|3.561000||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|2.071|8.024|4.707|10.126|-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||;CLINVAR_GROUND_TRUTH=Pathogenic;CADD=26.6;SPIDEX=-1.59;most_severe_consequence=329:G|missense_variant;Annotation=AGRN;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;VrsModelPrediction=0.49679;VrsModelExplanation=[] GT:DP:AD:GQ 1/1:30:4,26:38 -2 47403394 1784750 GAGAATGGGGGTGGGGGA TGCCCGCG . . CSQ=TGCCCGCG|intron_variant|MODIFIER|CALM2|ENSG00000143933|Transcript|ENST00000272298|protein_coding||1/5|ENST00000272298.7:c.3+169_3+186delinsCGCGGGCA|||||||||-1||HGNC|1445|YES|||CCDS1832.1|ENSP00000272298|CALM_HUMAN|Q96HY3_HUMAN&G3V361_HUMAN&B4DJ51_HUMAN|UPI00000000C1|||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|9.458|9.219||10.126|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|intron_variant|MODIFIER|CALM2|ENSG00000143933|Transcript|ENST00000409563|protein_coding||1/6|ENST00000409563.1:c.-72+169_-72+186delinsCGCGGGCA|||||||||-1||HGNC|1445|||||ENSP00000387065||Q96HY3_HUMAN&G3V361_HUMAN&E7EMB3_HUMAN|UPI00018815D8|||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|9.458|9.219||10.126|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|intron_variant&NMD_transcript_variant|MODIFIER|CALM2|ENSG00000143933|Transcript|ENST00000432899|nonsense_mediated_decay||1/4|ENST00000432899.1:c.3+169_3+186delinsCGCGGGCA|||||||||-1||HGNC|1445|||||ENSP00000406112||F8WBR5_HUMAN|UPI0001639110|||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|9.458|9.219||10.126|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|intron_variant|MODIFIER|CALM2|ENSG00000143933|Transcript|ENST00000456319|protein_coding||1/6|ENST00000456319.1:c.71+169_71+186delinsCGCGGGCA|||||||||-1|cds_start_NF|HGNC|1445|||||ENSP00000411440||Q96HY3_HUMAN&H0Y7A7_HUMAN&G3V361_HUMAN|UPI00018815D7|||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|8.486|10.998||10.126|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|upstream_gene_variant|MODIFIER|CALM2|ENSG00000143933|Transcript|ENST00000460218|retained_intron|||||||||||2048|-1||HGNC|1445|||||||||||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|||||2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|non_coding_transcript_exon_variant|MODIFIER|CALM2|ENSG00000143933|Transcript|ENST00000484408|processed_transcript|1/6||ENST00000484408.1:n.182_199delinsCGCGGGCA||182-199|||||||-1||HGNC|1445|||||||||||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|8.486|7.434|||2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|splice_donor_5th_base_variant&intron_variant&non_coding_transcript_variant|LOW|CALM2|ENSG00000143933|Transcript|ENST00000489742|processed_transcript||1/4|ENST00000489742.1:n.194+5_194+22delinsCGCGGGCA|||||||||-1||HGNC|1445|||||||||||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|8.486|10.998||3.602|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|intron_variant|MODIFIER|CALM2|805|Transcript|NM_001305624.1|protein_coding||1/6|NM_001305624.1:c.101+169_101+186delinsCGCGGGCA|||||||||-1||EntrezGene|1445|YES||||NP_001292553.1||||||RefSeq||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|OK||||||||||||||||||||||||||0.92|0.124|8.486|10.998||10.126|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|intron_variant|MODIFIER|CALM2|805|Transcript|NM_001305625.2|protein_coding||1/5|NM_001305625.2:c.-106+577_-106+594delinsCGCGGGCA|||||||||-1||EntrezGene|1445|||||NP_001292554.1||||||RefSeq||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|9.458|9.219||7.092|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|upstream_gene_variant|MODIFIER|CALM2|805|Transcript|NM_001305626.1|protein_coding|||||||||||2048|-1||EntrezGene|1445|||||NP_001292555.1||||||RefSeq||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|OK||||||||||||||||||||||||||0.92|0.124|||||2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|intron_variant|MODIFIER|CALM2|805|Transcript|NM_001743.6|protein_coding||1/5|NM_001743.6:c.3+169_3+186delinsCGCGGGCA|||||||||-1||EntrezGene|1445|||||NP_001734.1||||||RefSeq||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|9.458|9.219||10.126|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||;CLINVAR_GROUND_TRUTH=Likely_pathogenic;most_severe_consequence=1445:TGCCCGCG|splice_donor_5th_base_variant;Annotation=CALM2;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;VrsModelPrediction=0.82321;VrsModelExplanation=[] GT:DP:AD:GQ 1/1:30:4,26:38 -3 33114704 667634 C T . . CSQ=T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000307363|protein_coding||1/15|ENST00000307363.5:c.76-499G>A|||||||||-1||HGNC|4298|YES|||CCDS43061.1|ENSP00000306920|BGAL_HUMAN|C9JF15_HUMAN&C9J539_HUMAN|UPI0000E5A543|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000307377|protein_coding||1/12|ENST00000307377.8:c.76-499G>A|||||||||-1||HGNC|4298||||CCDS46785.1|ENSP00000305920||F8WF40_HUMAN&E7EQ29_HUMAN|UPI000049DF90|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000399402|protein_coding||1/15|ENST00000399402.3:c.-15-499G>A|||||||||-1||HGNC|4298||||CCDS43062.1|ENSP00000382333|BGAL_HUMAN|C9JF15_HUMAN&C9J539_HUMAN|UPI00015E0895|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||8.418|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000415454|protein_coding||1/5|ENST00000415454.1:c.76-14943G>A|||||||||-1|cds_end_NF|HGNC|4298|||||ENSP00000411813||C9J4G9_HUMAN|UPI000198C9CE|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|11.321|8.077||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000436768|protein_coding||2/3|ENST00000436768.1:c.220-499G>A|||||||||-1|cds_end_NF|HGNC|4298|||||ENSP00000387989||C9JWX1_HUMAN|UPI000198C9CB|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934|6.773|6.745|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000438227|nonsense_mediated_decay||1/4|ENST00000438227.1:c.76-7655G>A|||||||||-1||HGNC|4298|||||ENSP00000401250||F8WEN1_HUMAN|UPI000198C9CD|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|9.360|8.662||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000440656|protein_coding||1/4|ENST00000440656.1:c.-148-4242G>A|||||||||-1|cds_end_NF|HGNC|4298|||||ENSP00000411769||C9J539_HUMAN|UPI000198C9D1|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|9.815|10.126||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000445488|protein_coding||2/16|ENST00000445488.2:c.220-499G>A|||||||||-1||HGNC|4298|||||ENSP00000393377|BGAL_HUMAN|C9JWX1_HUMAN&C9JF15_HUMAN&C9J539_HUMAN|UPI00020654C3|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934|6.773|6.745|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|upstream_gene_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000446732|nonsense_mediated_decay|||||||||||497|-1||HGNC|4298|||||ENSP00000407365||F8WF40_HUMAN|UPI000198C9D0|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|||||-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000450835|protein_coding||2/3|ENST00000450835.1:c.-15-499G>A|||||||||-1|cds_end_NF|HGNC|4298|||||ENSP00000403264||C9JF15_HUMAN|UPI000198C9CC|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934|6.773|6.745|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000464355|processed_transcript||1/5|ENST00000464355.1:n.34-499G>A|||||||||-1||HGNC|4298|||||||||||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000482097|processed_transcript||1/6|ENST00000482097.1:n.109-19663G>A|||||||||-1||HGNC|4298|||||||||||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.346|8.846||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000485698|processed_transcript||1/5|ENST00000485698.1:n.137-19663G>A|||||||||-1||HGNC|4298|||||||||||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.346|8.846||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000498537|processed_transcript||1/5|ENST00000498537.1:n.133-19663G>A|||||||||-1||HGNC|4298|||||||||||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.346|8.846||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|2720|Transcript|NM_000404.4|protein_coding||1/15|NM_000404.4:c.76-499G>A|||||||||-1||EntrezGene|4298|||||NP_000395.3||||||RefSeq||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|2720|Transcript|NM_001079811.3|protein_coding||1/15|NM_001079811.3:c.-15-499G>A|||||||||-1||EntrezGene|4298|||||NP_001073279.2||||||RefSeq||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||8.418|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|2720|Transcript|NM_001135602.3|protein_coding||1/12|NM_001135602.3:c.76-499G>A|||||||||-1||EntrezGene|4298|||||NP_001129074.2||||||RefSeq||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|2720|Transcript|NM_001317040.2|protein_coding||2/16|NM_001317040.2:c.220-499G>A|||||||||-1||EntrezGene|4298|YES||||NP_001303969.2||||||RefSeq||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934|6.773|6.745|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||;CLINVAR_GROUND_TRUTH=Benign;CADD=2.843;most_severe_consequence=4298:T|intron_variant;Annotation=SUMO2P10,GLB1;VrsModelPrediction=0.00017;VrsModelExplanation=[] GT:DP:AD:GQ 0/0:30:4,26:38 -4 1803751 465358 A T . . CSQ=T|missense_variant&splice_region_variant|MODERATE|FGFR3|ENSG00000068078|Transcript|ENST00000260795|protein_coding|6/17||ENST00000260795.2:c.929A>T|ENSP00000260795.2:p.Lys310Met|1031|929|310|K/M|aAg/aTg|||1||HGNC|3690||||CCDS3353.1|ENSP00000260795|FGFR3_HUMAN|Q96T36_HUMAN&Q8NI15_HUMAN|UPI000012A72C|||Ensembl||A|A||deleterious|probably_damaging|Gene3D:2.60.40.10&Pfam:PF07679&PIRSF:PIRSF000628&PROSITE_profiles:PS50835&PANTHER:PTHR24416&PANTHER:PTHR24416:SF128&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726|||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|ENSG00000068078|Transcript|ENST00000340107|protein_coding|7/18||ENST00000340107.4:c.929A>T|ENSP00000339824.4:p.Lys310Met|1185|929|310|K/M|aAg/aTg|||1||HGNC|3690|YES|||CCDS54706.1|ENSP00000339824|FGFR3_HUMAN|Q8NI16_HUMAN|UPI000002A9AC|||Ensembl||A|A||deleterious|probably_damaging|Gene3D:2.60.40.10&Pfam:PF07679&PIRSF:PIRSF000628&PROSITE_profiles:PS50835&PANTHER:PTHR24416&PANTHER:PTHR24416:SF128&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726|||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|11.216|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|ENSG00000068078|Transcript|ENST00000352904|protein_coding|6/15||ENST00000352904.1:c.929A>T|ENSP00000231803.1:p.Lys310Met|968|929|310|K/M|aAg/aTg|||1||HGNC|3690||||CCDS3354.1|ENSP00000231803|FGFR3_HUMAN||UPI000002A9AD|||Ensembl||A|A||deleterious|probably_damaging|PIRSF:PIRSF000628&PANTHER:PTHR24416&PANTHER:PTHR24416:SF128&SMART:SM00409&Superfamily:SSF48726|||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|4.517|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|ENSG00000068078|Transcript|ENST00000412135|protein_coding|7/16||ENST00000412135.2:c.929A>T|ENSP00000412903.2:p.Lys310Met|1185|929|310|K/M|aAg/aTg|||1||HGNC|3690||||CCDS3354.1|ENSP00000412903|FGFR3_HUMAN||UPI000002A9AD|||Ensembl||A|A||deleterious|probably_damaging|PIRSF:PIRSF000628&PANTHER:PTHR24416&PANTHER:PTHR24416:SF128&SMART:SM00409&Superfamily:SSF48726|||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|4.517|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|ENSG00000068078|Transcript|ENST00000440486|protein_coding|7/18||ENST00000440486.2:c.929A>T|ENSP00000414914.2:p.Lys310Met|1185|929|310|K/M|aAg/aTg|||1||HGNC|3690||||CCDS3353.1|ENSP00000414914|FGFR3_HUMAN|Q96T36_HUMAN&Q8NI15_HUMAN|UPI000012A72C|||Ensembl||A|A||deleterious|probably_damaging|Gene3D:2.60.40.10&Pfam:PF07679&PIRSF:PIRSF000628&PROSITE_profiles:PS50835&PANTHER:PTHR24416&PANTHER:PTHR24416:SF128&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726|||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|upstream_gene_variant|MODIFIER|FGFR3|ENSG00000068078|Transcript|ENST00000469068|retained_intron|||||||||||2468|1||HGNC|3690|||||||||||Ensembl||A|A||||||||||||||||||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|||||-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926||||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|FGFR3|ENSG00000068078|Transcript|ENST00000474521|processed_transcript|2/3||ENST00000474521.1:n.305A>T||305|||||||1||HGNC|3690|||||||||||Ensembl||A|A||||||||||||||||||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|11.216|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|ENSG00000068078|Transcript|ENST00000481110|protein_coding|7/17||ENST00000481110.2:c.929A>T|ENSP00000420533.2:p.Lys310Met|1190|929|310|K/M|aAg/aTg|||1||HGNC|3690|||||ENSP00000420533||Q96T36_HUMAN&F8W9L4_HUMAN|UPI00016394EA|||Ensembl||A|A||deleterious|probably_damaging|Gene3D:2.60.40.10&Pfam:PF07679&PROSITE_profiles:PS50835&PANTHER:PTHR24416&PANTHER:PTHR24416:SF128&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726&PIRSF:PIRSF000628|||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|intron_variant|MODIFIER|FGFR3|ENSG00000068078|Transcript|ENST00000507588|protein_coding||3/3|ENST00000507588.1:c.288+101A>T|||||||||1|cds_start_NF&cds_end_NF|HGNC|3690|||||ENSP00000427289||Q96T34_HUMAN|UPI000006D430|||Ensembl||A|A||||||||||||||||||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955||8.067|2.411|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926||||||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|2261|Transcript|NM_000142.5|protein_coding|7/18||NM_000142.5:c.929A>T|NP_000133.1:p.Lys310Met|1204|929|310|K/M|aAg/aTg|||1||EntrezGene|3690|||||NP_000133.1||||||RefSeq||A|A||deleterious|probably_damaging||||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|7/18||NM_001163213.2:c.929A>T|NP_001156685.1:p.Lys310Met|1204|929|310|K/M|aAg/aTg|||1||EntrezGene|3690|YES||||NP_001156685.1||||||RefSeq||A|A||deleterious|probably_damaging||||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|11.216|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|7/18||NM_001354809.2:c.929A>T|NP_001341738.1:p.Lys310Met|1204|929|310|K/M|aAg/aTg|||1||EntrezGene|3690|||||NP_001341738.1||||||RefSeq||A|A|||||||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|7/17||NM_001354810.2:c.929A>T|NP_001341739.1:p.Lys310Met|1204|929|310|K/M|aAg/aTg|||1||EntrezGene|3690|||||NP_001341739.1||||||RefSeq||A|A||deleterious|probably_damaging||||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|2261|Transcript|NM_022965.4|protein_coding|7/16||NM_022965.4:c.929A>T|NP_075254.1:p.Lys310Met|1204|929|310|K/M|aAg/aTg|||1||EntrezGene|3690|||||NP_075254.1||||||RefSeq||A|A||deleterious|probably_damaging||||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|4.517|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|7/19||NR_148971.2:n.1204A>T||1204|||||||1||EntrezGene|3690|||||||||||RefSeq||A|A||||||||||||||||||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|11.216|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||;CADD=33;CLINVAR_GROUND_TRUTH=Benign;SPIDEX=-1.441;most_severe_consequence=3690:T|missense_variant;Annotation=FGFR3;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;VrsModelPrediction=0.99434;VrsModelExplanation=[CADD=0.28,CSQ_REVEL_score=0.25,GNOMADAF_popmax=0.12,most_severe_consequence=0.09,SWEGENAF=0.09,CSQ_CLINVAR_CLNSIG=0.08,CSQ_SIFT=0.05,CSQ_phyloP100way_vertebrate=0.05,CSQ_SpliceAI_pred_DS_DG=0.03,CSQ_MES-SWA_donor_alt=0.02,Frq=0.02,CSQ_SpliceAI_pred_DS_DL=0.02,CSQ_MES-SWA_donor_diff=0.01,CSQ_SpliceAI_pred_DS_AL=0.00,CSQ_MES-SWA_acceptor_alt=0.00,CSQ_CLINVAR_CLNREVSTAT=0.00,CSQ_SpliceAI_pred_DS_AG=0.00,CSQ_LoFtool=-0.00,CSQ_MaxEntScan_diff=-0.01,CSQ_MaxEntScan_alt=-0.01,CSQ_GERP++_RS=-0.02,CSQ_phastCons100way_vertebrate=-0.02,CSQ_PolyPhen=-0.07,] GT:DP:AD:GQ 1/1:30:4,26:38 -5 45645297 1341556 T G . . CSQ=G|missense_variant|MODERATE|HCN1|ENSG00000164588|Transcript|ENST00000303230|protein_coding|2/8||ENST00000303230.4:c.839A>C|ENSP00000307342.4:p.Gln280Pro|897|839|280|Q/P|cAa/cCa|||-1||HGNC|4845|YES|||CCDS3952.1|ENSP00000307342|HCN1_HUMAN||UPI00001AED69|||Ensembl||T|T||deleterious|benign|Gene3D:1.10.287.70&Pfam:PF00520&PANTHER:PTHR10217&PANTHER:PTHR10217:SF373&Superfamily:SSF81324|||||||5.5|5.5|0.94360|0.821|1.000000|8.017000||20|11|-10|-9|0.00|0.00|0.02|0.00|HCN1|1.00|0.111|8.073|10.065|9.192|10.068|-3.359|-1.672|-5.030|-5.030|-9.949|-0.759|-10.708|-10.708||||||||,G|missense_variant|MODERATE|HCN1|348980|Transcript|NM_021072.4|protein_coding|2/8||NM_021072.4:c.839A>C|NP_066550.2:p.Gln280Pro|1126|839|280|Q/P|cAa/cCa|||-1||EntrezGene|4845|YES||||NP_066550.2||||||RefSeq||T|T||deleterious|benign||||||||5.5|5.5|0.94360|0.821|1.000000|8.017000||20|11|-10|-9|0.00|0.00|0.02|0.00|HCN1|1.00|0.111|8.073|10.065|9.192|10.068|-3.359|-1.672|-5.030|-5.030|-9.949|-0.759|-10.708|-10.708||||||||;CLINVAR_GROUND_TRUTH=Pathogenic;CADD=24;SPIDEX=-0.417;most_severe_consequence=4845:G|missense_variant;Annotation=HCN1;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;VrsModelPrediction=0.97249;VrsModelExplanation=[CSQ_REVEL_score=0.42,GNOMADAF_popmax=0.13,CADD=0.12,SWEGENAF=0.11,most_severe_consequence=0.10,CSQ_CLINVAR_CLNSIG=0.09,CSQ_phyloP100way_vertebrate=0.04,CSQ_SIFT=0.04,Frq=0.02,CSQ_MES-SWA_acceptor_alt=0.00,CSQ_SpliceAI_pred_DS_AG=0.00,CSQ_SpliceAI_pred_DS_AL=0.00,CSQ_MES-SWA_donor_diff=0.00,CSQ_MES-SWA_donor_alt=0.00,CSQ_LoFtool=0.00,CSQ_MaxEntScan_diff=0.00,CSQ_MaxEntScan_alt=0.00,CSQ_SpliceAI_pred_DS_DG=0.00,CSQ_SpliceAI_pred_DS_DL=-0.01,CSQ_GERP++_RS=-0.01,CSQ_CLINVAR_CLNREVSTAT=-0.02,CSQ_phastCons100way_vertebrate=-0.02,CSQ_PolyPhen=-0.06,] GT:DP:AD:GQ 1/1:30:4,26:38 -5 45645306 635188 T C . . CSQ=C|missense_variant|MODERATE|HCN1|ENSG00000164588|Transcript|ENST00000303230|protein_coding|2/8||ENST00000303230.4:c.830A>G|ENSP00000307342.4:p.Tyr277Cys|888|830|277|Y/C|tAc/tGc|||-1||HGNC|4845|YES|||CCDS3952.1|ENSP00000307342|HCN1_HUMAN||UPI00001AED69|||Ensembl||T|T||deleterious|probably_damaging|Gene3D:1.10.287.70&Pfam:PF00520&PANTHER:PTHR10217&PANTHER:PTHR10217:SF373&Superfamily:SSF81324|||||||5.5|5.5|0.99415|0.961|1.000000|8.017000||11|-19|-19|12|0.00|0.00|0.05|0.00|HCN1|1.00|0.111|8.073|10.065|9.192|10.068|-2.879|-0.050|-2.929|-2.929|-7.371|3.551|-3.820|-3.820||||||||,C|missense_variant|MODERATE|HCN1|348980|Transcript|NM_021072.4|protein_coding|2/8||NM_021072.4:c.830A>G|NP_066550.2:p.Tyr277Cys|1117|830|277|Y/C|tAc/tGc|||-1||EntrezGene|4845|YES||||NP_066550.2||||||RefSeq||T|T||deleterious|probably_damaging||||||||5.5|5.5|0.99415|0.961|1.000000|8.017000||11|-19|-19|12|0.00|0.00|0.05|0.00|HCN1|1.00|0.111|8.073|10.065|9.192|10.068|-2.879|-0.050|-2.929|-2.929|-7.371|3.551|-3.820|-3.820||||||||;CLINVAR_GROUND_TRUTH=Pathogenic;CADD=29.2;SPIDEX=0.253;most_severe_consequence=4845:C|missense_variant;Annotation=HCN1;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;VrsModelPrediction=0.99276;VrsModelExplanation=[CSQ_REVEL_score=0.41,CADD=0.15,GNOMADAF_popmax=0.13,most_severe_consequence=0.11,SWEGENAF=0.11,CSQ_CLINVAR_CLNSIG=0.08,CSQ_SIFT=0.05,CSQ_phyloP100way_vertebrate=0.04,Frq=0.02,CSQ_SpliceAI_pred_DS_AG=0.01,CSQ_MaxEntScan_alt=0.00,CSQ_SpliceAI_pred_DS_AL=0.00,CSQ_SpliceAI_pred_DS_DG=0.00,CSQ_MES-SWA_donor_diff=0.00,CSQ_LoFtool=0.00,CSQ_MES-SWA_acceptor_alt=0.00,CSQ_MaxEntScan_diff=0.00,CSQ_SpliceAI_pred_DS_DL=-0.00,CSQ_MES-SWA_donor_alt=-0.01,CSQ_CLINVAR_CLNREVSTAT=-0.01,CSQ_phastCons100way_vertebrate=-0.02,CSQ_GERP++_RS=-0.02,CSQ_PolyPhen=-0.06,] GT:DP:AD:GQ 1/1:30:4,26:38 -6 7580872 1072470 A ACT . . CSQ=CT|frameshift_variant|HIGH|DSP|ENSG00000096696|Transcript|ENST00000379802|protein_coding|23/24||ENST00000379802.3:c.4449_4450insCT|ENSP00000369129.3:p.Glu1484LeufsTer4|4790-4791|4449-4450|1483-1484|-/X|-/CT|||1||HGNC|3052|YES|||CCDS4501.1|ENSP00000369129|DESP_HUMAN|G1UI31_HUMAN&B4DKX6_HUMAN|UPI000013C67F|||Ensembl|||||||Coiled-coils_(Ncoils):Coil&PANTHER:PTHR11915:SF234&PANTHER:PTHR11915|||||||||||||||||||||||1.00|0.077|10.540|6.347|9.971|8.829|-9.260|-1.245|-10.504|-10.504|-0.510|-3.129|-3.639|-3.639||||||||,CT|intron_variant|MODIFIER|DSP|ENSG00000096696|Transcript|ENST00000418664|protein_coding||23/23|ENST00000418664.2:c.3582+867_3582+868insCT|||||||||1||HGNC|3052||||CCDS47368.1|ENSP00000396591|DESP_HUMAN|Q4LE79_HUMAN&G1UI31_HUMAN&B4DKX6_HUMAN|UPI00004C9B0E|||Ensembl||||||||||||||||||||||||||||||1.00|0.077|10.540||9.971|10.567|-9.260|-1.245|-10.504|-10.504|-0.510|-3.129|-3.639|-3.639||||||||,CT|intron_variant|MODIFIER|DSP|1832|Transcript|NM_001008844.3|protein_coding||23/23|NM_001008844.3:c.3582+867_3582+868insCT|||||||||1||EntrezGene|3052|||||NP_001008844.1||||||RefSeq||||OK||||||||||||||||||||||||||1.00|0.077|10.540||9.971|10.567|-9.260|-1.245|-10.504|-10.504|-0.510|-3.129|-3.639|-3.639||||||||,CT|intron_variant|MODIFIER|DSP|1832|Transcript|NM_001319034.2|protein_coding||23/23|NM_001319034.2:c.4050+399_4050+400insCT|||||||||1||EntrezGene|3052|||||NP_001305963.1||||||RefSeq||||OK||||||||||||||||||||||||||1.00|0.077|10.540||9.971|10.567|-9.260|-1.245|-10.504|-10.504|-0.510|-3.129|-3.639|-3.639||||||||,CT|frameshift_variant|HIGH|DSP|1832|Transcript|NM_004415.4|protein_coding|23/24||NM_004415.4:c.4449_4450insCT|NP_004406.2:p.Glu1484LeufsTer4|4694-4695|4449-4450|1483-1484|-/X|-/CT|||1||EntrezGene|3052|YES||||NP_004406.2||||||RefSeq||||OK||||||||||||||||||||||||||1.00|0.077|10.540|6.347|9.971|8.829|-9.260|-1.245|-10.504|-10.504|-0.510|-3.129|-3.639|-3.639||||||||;CADD=33;CLINVAR_GROUND_TRUTH=Pathogenic;most_severe_consequence=3052:CT|frameshift_variant;Annotation=DSP;VrsModelPrediction=0.99743;VrsModelExplanation=[most_severe_consequence=0.39,CADD=0.27,GNOMADAF_popmax=0.13,SWEGENAF=0.10,CSQ_CLINVAR_CLNSIG=0.10,Frq=0.01,CSQ_MES-SWA_acceptor_alt=0.01,CSQ_SpliceAI_pred_DS_AG=0.00,CSQ_MaxEntScan_alt=0.00,CSQ_MES-SWA_donor_alt=0.00,CSQ_SIFT=0.00,CSQ_PolyPhen=0.00,CSQ_phyloP100way_vertebrate=0.00,CSQ_MaxEntScan_diff=0.00,CSQ_phastCons100way_vertebrate=0.00,CSQ_LoFtool=0.00,CSQ_GERP++_RS=0.00,CSQ_REVEL_score=0.00,CSQ_SpliceAI_pred_DS_DL=0.00,CSQ_SpliceAI_pred_DS_AL=0.00,CSQ_MES-SWA_donor_diff=0.00,CSQ_SpliceAI_pred_DS_DG=0.00,CSQ_CLINVAR_CLNREVSTAT=-0.02,] GT:DP:AD:GQ 0/0:30:4,26:38 -6 7580957 923905 T C . . CSQ=C|missense_variant|MODERATE|DSP|ENSG00000096696|Transcript|ENST00000379802|protein_coding|23/24||ENST00000379802.3:c.4534T>C|ENSP00000369129.3:p.Tyr1512His|4875|4534|1512|Y/H|Tat/Cat|||1||HGNC|3052|YES|||CCDS4501.1|ENSP00000369129|DESP_HUMAN|G1UI31_HUMAN&B4DKX6_HUMAN|UPI000013C67F|||Ensembl||T|T||tolerated|possibly_damaging|Coiled-coils_(Ncoils):Coil&PANTHER:PTHR11915:SF234&PANTHER:PTHR11915|||||||5.74|3.3|0.21181|0.071|0.260000|0.431000|rs779987722|-29|23|21|-7|0.00|0.00|0.00|0.00|DSP|1.00|0.077|10.540|6.347|9.971|8.829|0.598|0.309|0.907|0.907|-5.393|7.754|2.361|2.361||||||||,C|intron_variant|MODIFIER|DSP|ENSG00000096696|Transcript|ENST00000418664|protein_coding||23/23|ENST00000418664.2:c.3582+952T>C|||||||||1||HGNC|3052||||CCDS47368.1|ENSP00000396591|DESP_HUMAN|Q4LE79_HUMAN&G1UI31_HUMAN&B4DKX6_HUMAN|UPI00004C9B0E|||Ensembl||T|T||||||||||||||||||-29|23|21|-7|0.00|0.00|0.00|0.00|DSP|1.00|0.077|10.540||9.971|10.567|0.598|0.309|0.907|0.907|-5.393|7.754|2.361|2.361||||||||,C|intron_variant|MODIFIER|DSP|1832|Transcript|NM_001008844.3|protein_coding||23/23|NM_001008844.3:c.3582+952T>C|||||||||1||EntrezGene|3052|||||NP_001008844.1||||||RefSeq||T|T|OK|||||||||||||||||-29|23|21|-7|0.00|0.00|0.00|0.00|DSP|1.00|0.077|10.540||9.971|10.567|0.598|0.309|0.907|0.907|-5.393|7.754|2.361|2.361||||||||,C|intron_variant|MODIFIER|DSP|1832|Transcript|NM_001319034.2|protein_coding||23/23|NM_001319034.2:c.4050+484T>C|||||||||1||EntrezGene|3052|||||NP_001305963.1||||||RefSeq||T|T|OK|||||||||||||||||-29|23|21|-7|0.00|0.00|0.00|0.00|DSP|1.00|0.077|10.540||9.971|10.567|0.598|0.309|0.907|0.907|-5.393|7.754|2.361|2.361||||||||,C|missense_variant|MODERATE|DSP|1832|Transcript|NM_004415.4|protein_coding|23/24||NM_004415.4:c.4534T>C|NP_004406.2:p.Tyr1512His|4779|4534|1512|Y/H|Tat/Cat|||1||EntrezGene|3052|YES||||NP_004406.2||||||RefSeq||T|T|OK|tolerated|possibly_damaging||||||||5.74|3.3|0.21181|0.071|0.260000|0.431000|rs779987722|-29|23|21|-7|0.00|0.00|0.00|0.00|DSP|1.00|0.077|10.540|6.347|9.971|8.829|0.598|0.309|0.907|0.907|-5.393|7.754|2.361|2.361||||||||;SPIDEX=-0.068;CADD=15.86;CLINVAR_GROUND_TRUTH=Benign/Likely_benign;most_severe_consequence=3052:C|missense_variant;Annotation=DSP;VrsModelPrediction=0.05780;VrsModelExplanation=[] GT:DP:AD:GQ 0/0:30:4,26:38 -7 50458565 360425 T G . . CSQ=G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000331340|protein_coding||6/7|ENST00000331340.3:c.716-862T>G|||||||||1||HGNC|13176|||||ENSP00000331614|IKZF1_HUMAN||UPI000012D465|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000343574|protein_coding||5/6|ENST00000343574.5:c.455-862T>G|||||||||1||HGNC|13176|||||ENSP00000342750|IKZF1_HUMAN||UPI000002ABB9|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000346667|protein_coding||3/3|ENST00000346667.4:c.161-9051T>G|||||||||1||HGNC|13176|||||ENSP00000340080|IKZF1_HUMAN|Q3T907_HUMAN|UPI000002ABBD|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.743|10.239|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000349824|protein_coding||4/4|ENST00000349824.4:c.422-9051T>G|||||||||1||HGNC|13176||||CCDS69299.1|ENSP00000342485|IKZF1_HUMAN||UPI000002ABBC|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||8.553|9.675|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000357364|protein_coding||5/5|ENST00000357364.4:c.589+8160T>G|||||||||1||HGNC|13176|||||ENSP00000349928|IKZF1_HUMAN||UPI000002ABBA|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000359197|protein_coding||5/6|ENST00000359197.5:c.590-862T>G|||||||||1||HGNC|13176||||CCDS59055.1|ENSP00000352123|IKZF1_HUMAN||UPI000002ABBE|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000426121|protein_coding||1/1|ENST00000426121.1:c.110-9051T>G|||||||||1|cds_start_NF&cds_end_NF|HGNC|13176|||||ENSP00000409588||Q3T907_HUMAN|UPI00005B2C77|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010|||10.239|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000438033|protein_coding||5/6|ENST00000438033.1:c.455-862T>G|||||||||1||HGNC|13176|||||ENSP00000396554|IKZF1_HUMAN||UPI000002ABB9|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000439701|protein_coding||5/6|ENST00000439701.1:c.590-862T>G|||||||||1||HGNC|13176|YES|||CCDS59055.1|ENSP00000413025|IKZF1_HUMAN||UPI000002ABBE|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000440768|protein_coding||5/7|ENST00000440768.2:c.590-862T>G|||||||||1||HGNC|13176|||||ENSP00000401507|IKZF1_HUMAN||UPI0000401AEF|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|-5.489|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000471793|retained_intron||4/5|ENST00000471793.1:n.935-862T>G|||||||||1||HGNC|13176|||||||||||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220765.3|protein_coding||5/6|NM_001220765.3:c.590-862T>G|||||||||1||EntrezGene|13176|||||NP_001207694.1||||||RefSeq||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220767.2|protein_coding||4/5|NM_001220767.2:c.455-862T>G|||||||||1||EntrezGene|13176|||||NP_001207696.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|7.688|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220768.2|protein_coding||4/4|NM_001220768.2:c.589+8160T>G|||||||||1||EntrezGene|13176|||||NP_001207697.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220770.2|protein_coding||3/4|NM_001220770.2:c.329-862T>G|||||||||1||EntrezGene|13176|||||NP_001207699.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|7.688|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220771.2|protein_coding||3/3|NM_001220771.2:c.422-9051T>G|||||||||1||EntrezGene|13176|||||NP_001207700.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||8.553|9.675|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291837.2|protein_coding||5/6|NM_001291837.2:c.590-862T>G|||||||||1||EntrezGene|13176|||||NP_001278766.1||||||RefSeq||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291838.2|protein_coding||5/6|NM_001291838.2:c.455-862T>G|||||||||1||EntrezGene|13176|||||NP_001278767.1||||||RefSeq||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291839.2|protein_coding||4/5|NM_001291839.2:c.329-862T>G|||||||||1||EntrezGene|13176|||||NP_001278768.1||||||RefSeq||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291840.1|protein_coding||2/2|NM_001291840.1:c.161-9051T>G|||||||||1||EntrezGene|13176|||||NP_001278769.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.743|10.239|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291841.1|protein_coding||3/4|NM_001291841.1:c.287-862T>G|||||||||1||EntrezGene|13176|||||NP_001278770.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291842.1|protein_coding||3/4|NM_001291842.1:c.287-862T>G|||||||||1||EntrezGene|13176|||||NP_001278771.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|7.688|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291843.1|protein_coding||2/3|NM_001291843.1:c.161-862T>G|||||||||1||EntrezGene|13176|||||NP_001278772.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|9.743|10.239|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291844.1|protein_coding||2/3|NM_001291844.1:c.161-862T>G|||||||||1||EntrezGene|13176|||||NP_001278773.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|7.688|9.743|10.239|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_006060.6|protein_coding||6/7|NM_006060.6:c.716-862T>G|||||||||1||EntrezGene|13176|YES||||NP_006051.1||||||RefSeq||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||;CADD=3.134;CLINVAR_GROUND_TRUTH=Benign;most_severe_consequence=13176:G|intron_variant;Annotation=IKZF1;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;VrsModelPrediction=0.00017;VrsModelExplanation=[] GT:DP:AD:GQ 1/1:30:4,26:38 -7 50463289 2136536 C G . . CSQ=G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000331340|protein_coding||7/7|ENST00000331340.3:c.850+3728C>G|||||||||1||HGNC|13176|||||ENSP00000331614|IKZF1_HUMAN||UPI000012D465|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000343574|protein_coding||6/6|ENST00000343574.5:c.589+3728C>G|||||||||1||HGNC|13176|||||ENSP00000342750|IKZF1_HUMAN||UPI000002ABB9|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000346667|protein_coding||3/3|ENST00000346667.4:c.161-4327C>G|||||||||1||HGNC|13176|||||ENSP00000340080|IKZF1_HUMAN|Q3T907_HUMAN|UPI000002ABBD|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.743|10.239|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000349824|protein_coding||4/4|ENST00000349824.4:c.422-4327C>G|||||||||1||HGNC|13176||||CCDS69299.1|ENSP00000342485|IKZF1_HUMAN||UPI000002ABBC|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||8.553|9.675|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000357364|protein_coding||5/5|ENST00000357364.4:c.590-4327C>G|||||||||1||HGNC|13176|||||ENSP00000349928|IKZF1_HUMAN||UPI000002ABBA|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.944|9.394|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000359197|protein_coding||6/6|ENST00000359197.5:c.724+3728C>G|||||||||1||HGNC|13176||||CCDS59055.1|ENSP00000352123|IKZF1_HUMAN||UPI000002ABBE|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000426121|protein_coding||1/1|ENST00000426121.1:c.110-4327C>G|||||||||1|cds_start_NF&cds_end_NF|HGNC|13176|||||ENSP00000409588||Q3T907_HUMAN|UPI00005B2C77|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010|||10.239|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000438033|protein_coding||6/6|ENST00000438033.1:c.589+3728C>G|||||||||1||HGNC|13176|||||ENSP00000396554|IKZF1_HUMAN||UPI000002ABB9|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000439701|protein_coding||6/6|ENST00000439701.1:c.724+3728C>G|||||||||1||HGNC|13176|YES|||CCDS59055.1|ENSP00000413025|IKZF1_HUMAN||UPI000002ABBE|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000440768|protein_coding||7/7|ENST00000440768.2:c.*41+3728C>G|||||||||1||HGNC|13176|||||ENSP00000401507|IKZF1_HUMAN||UPI0000401AEF|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||-29.410|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000471793|retained_intron||5/5|ENST00000471793.1:n.1069+3728C>G|||||||||1||HGNC|13176|||||||||||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220765.3|protein_coding||6/6|NM_001220765.3:c.724+3728C>G|||||||||1||EntrezGene|13176|||||NP_001207694.1||||||RefSeq||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220767.2|protein_coding||5/5|NM_001220767.2:c.559+3758C>G|||||||||1||EntrezGene|13176|||||NP_001207696.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|7.688|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220768.2|protein_coding||4/4|NM_001220768.2:c.590-4327C>G|||||||||1||EntrezGene|13176|||||NP_001207697.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.944|9.394|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220770.2|protein_coding||4/4|NM_001220770.2:c.433+3758C>G|||||||||1||EntrezGene|13176|||||NP_001207699.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|7.688|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220771.2|protein_coding||3/3|NM_001220771.2:c.422-4327C>G|||||||||1||EntrezGene|13176|||||NP_001207700.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||8.553|9.675|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291837.2|protein_coding||6/6|NM_001291837.2:c.724+3728C>G|||||||||1||EntrezGene|13176|||||NP_001278766.1||||||RefSeq||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291838.2|protein_coding||6/6|NM_001291838.2:c.589+3728C>G|||||||||1||EntrezGene|13176|||||NP_001278767.1||||||RefSeq||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291839.2|protein_coding||5/5|NM_001291839.2:c.463+3728C>G|||||||||1||EntrezGene|13176|||||NP_001278768.1||||||RefSeq||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291840.1|protein_coding||2/2|NM_001291840.1:c.161-4327C>G|||||||||1||EntrezGene|13176|||||NP_001278769.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.743|10.239|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291841.1|protein_coding||4/4|NM_001291841.1:c.421+3728C>G|||||||||1||EntrezGene|13176|||||NP_001278770.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291842.1|protein_coding||4/4|NM_001291842.1:c.391+3758C>G|||||||||1||EntrezGene|13176|||||NP_001278771.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|7.688|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291843.1|protein_coding||3/3|NM_001291843.1:c.295+3728C>G|||||||||1||EntrezGene|13176|||||NP_001278772.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291844.1|protein_coding||3/3|NM_001291844.1:c.265+3758C>G|||||||||1||EntrezGene|13176|||||NP_001278773.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|7.688|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_006060.6|protein_coding||7/7|NM_006060.6:c.850+3728C>G|||||||||1||EntrezGene|13176|YES||||NP_006051.1||||||RefSeq||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||;CADD=4.931;CLINVAR_GROUND_TRUTH=Pathogenic;most_severe_consequence=13176:G|intron_variant;Annotation=IKZF1;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;VrsModelPrediction=0.00023;VrsModelExplanation=[] GT:DP:AD:GQ 1/1:30:4,26:38 -9 13193319 1657520 A AG . . CSQ=G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000319217|protein_coding||13/46|ENST00000319217.7:c.1657-8dup|||||||||-1||HGNC|7208|||||ENSP00000320006|MPDZ_HUMAN|B3KRN5_HUMAN&B3KQC9_HUMAN|UPI0000211133|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000381015|protein_coding||12/45|ENST00000381015.4:c.1657-8dup|||||||||-1||HGNC|7208|||||ENSP00000370403|MPDZ_HUMAN|B3KRN5_HUMAN&B3KQC9_HUMAN|UPI0000211133|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000381022|protein_coding||12/44|ENST00000381022.2:c.1657-8dup|||||||||-1||HGNC|7208||||CCDS47951.1|ENSP00000370410|MPDZ_HUMAN||UPI00015367D3|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000447879|protein_coding||12/44|ENST00000447879.1:c.1657-8dup|||||||||-1||HGNC|7208||||CCDS59120.1|ENSP00000415208|MPDZ_HUMAN|B7ZB24_HUMAN&B3KRN5_HUMAN&B3KQC9_HUMAN|UPI0000151582|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000536827|protein_coding||12/43|ENST00000536827.1:c.1657-8dup|||||||||-1||HGNC|7208||||CCDS59119.1|ENSP00000444151|MPDZ_HUMAN||UPI000191706B|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|upstream_gene_variant|MODIFIER|MPDZ|ENSG00000107186|Transcript|ENST00000539508|retained_intron|||||||||||3143|-1||HGNC|7208|||||||||||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|||||14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000541718|protein_coding||13/45|ENST00000541718.1:c.1657-8dup|||||||||-1||HGNC|7208|YES|||CCDS47951.1|ENSP00000439807|MPDZ_HUMAN||UPI00015367D3|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000546205|protein_coding||13/47|ENST00000546205.1:c.1657-8dup|||||||||-1||HGNC|7208|||||ENSP00000446358||F5H1U9_HUMAN&B3KRN5_HUMAN&B3KQC9_HUMAN|UPI000204A742|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001261406.2|protein_coding||13/45|NM_001261406.2:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001248335.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001261407.2|protein_coding||13/44|NM_001261407.2:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001248336.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001330637.2|protein_coding||13/46|NM_001330637.2:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001317566.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375413.1|protein_coding||13/47|NM_001375413.1:c.1657-8dup|||||||||-1||EntrezGene|7208|YES||||NP_001362342.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375416.1|protein_coding||13/45|NM_001375416.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362345.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375417.1|protein_coding||13/45|NM_001375417.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362346.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375418.1|protein_coding||14/46|NM_001375418.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362347.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375419.1|protein_coding||13/44|NM_001375419.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362348.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375420.1|protein_coding||13/44|NM_001375420.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362349.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375421.1|protein_coding||14/45|NM_001375421.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362350.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375422.1|protein_coding||13/44|NM_001375422.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362351.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375423.1|protein_coding||14/45|NM_001375423.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362352.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375424.1|protein_coding||13/44|NM_001375424.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362353.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375425.1|protein_coding||13/43|NM_001375425.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362354.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375426.1|protein_coding||13/43|NM_001375426.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362355.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375427.1|protein_coding||13/42|NM_001375427.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362356.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001378778.1|protein_coding||13/46|NM_001378778.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001365707.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_003829.5|protein_coding||13/45|NM_003829.5:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_003820.2||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||;CLINVAR_GROUND_TRUTH=Benign;CADD=6.052;most_severe_consequence=7208:G|splice_region_variant;Annotation=MPDZ;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;VrsModelPrediction=0.00437;VrsModelExplanation=[] GT:DP:AD:GQ 1/1:30:4,26:38 -19 13207585 1172824 A C . . CSQ=C|downstream_gene_variant|MODIFIER|LYL1|ENSG00000104903|Transcript|ENST00000264824|protein_coding|||||||||||2262|-1||HGNC|6734|YES|||CCDS12292.1|ENSP00000264824|LYL1_HUMAN|K7ER61_HUMAN|UPI000013D576|||Ensembl||A|A|||||||||||||||||||||||||||0.77||||||-0.225|0.223|-0.001|-0.001|-13.766|3.716|-10.051|-10.051||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000358552|protein_coding|9/9||ENST00000358552.3:c.*2122A>C||3505|||||||1||HGNC|7788|||||ENSP00000351354||K7ESG9_HUMAN&K7EKH0_HUMAN&C9JWJ8_HUMAN|UPI0000456C1A|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000360105|protein_coding|9/9||ENST00000360105.4:c.*2157A>C||3434|||||||1||HGNC|7788|||||ENSP00000353219||K7ESG9_HUMAN&K7EKH0_HUMAN|UPI0000366D41|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000397661|protein_coding|||||||||||570|1||HGNC|7788|YES|||CCDS45996.1|ENSP00000380781|NFIX_HUMAN|K7ESG9_HUMAN&K7EKH0_HUMAN|UPI000002AF1D|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000585575|protein_coding|||||||||||2122|1||HGNC|7788|||||ENSP00000468794|NFIX_HUMAN|K7ESG9_HUMAN&K7EN08_HUMAN&K7EKH0_HUMAN&D2DXM9_HUMAN|UPI000002AF1E|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000586797|nonsense_mediated_decay|||||||||||2087|1||HGNC|7788|||||ENSP00000467536||K7EPU2_HUMAN|UPI0002840A61|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000587260|protein_coding|||||||||||2001|1||HGNC|7788|||||ENSP00000467785|NFIX_HUMAN|K7ESG9_HUMAN&K7EKH0_HUMAN|UPI000002AF1F|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000587760|protein_coding|||||||||||2013|1||HGNC|7788||||CCDS59359.1|ENSP00000466389|NFIX_HUMAN|K7ESG9_HUMAN&K7EKH0_HUMAN|UPI000003B460|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000588228|protein_coding|||||||||||2016|1||HGNC|7788|||||ENSP00000466735||K7ESG9_HUMAN&K7EN08_HUMAN&K7EKH0_HUMAN|UPI00006DE7B6|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|LYL1|ENSG00000104903|Transcript|ENST00000590120|retained_intron|||||||||||4407|-1||HGNC|6734|||||||||||Ensembl||A|A|||||||||||||||||||||||||||0.77||||||-0.225|0.223|-0.001|-0.001|-13.766|3.716|-10.051|-10.051||||||||,C|downstream_gene_variant|MODIFIER|LYL1|ENSG00000104903|Transcript|ENST00000590974|protein_coding|||||||||||3919|-1|cds_end_NF|HGNC|6734|||||ENSP00000468122||K7ER61_HUMAN|UPI0002840A94|||Ensembl||A|A|||||||||||||||||||||||||||0.77||||||-0.225|0.223|-0.001|-0.001|-13.766|3.716|-10.051|-10.051||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000592199|protein_coding|||||||||||2122|1||HGNC|7788|||||ENSP00000467512|NFIX_HUMAN|K7ESG9_HUMAN&K7EN08_HUMAN&K7EKH0_HUMAN|UPI000012FFCC|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001271043.2|protein_coding|11/11||NM_001271043.2:c.*2122A>C||3708|||||||1||EntrezGene|7788|||||NP_001257972.1||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001271044.3|protein_coding|10/10||NM_001271044.3:c.*2157A>C||3519|||||||1||EntrezGene|7788|||||NP_001257973.1||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001365902.3|protein_coding|11/11||NM_001365902.3:c.*2122A>C||3994|||||||1||EntrezGene|7788|||||NP_001352831.1||||||RefSeq||A|A|||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001365982.2|protein_coding|9/9||NM_001365982.2:c.*2157A>C||3723|||||||1||EntrezGene|7788|||||NP_001352911.1||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001365983.2|protein_coding|10/10||NM_001365983.2:c.*2157A>C||3560|||||||1||EntrezGene|7788|||||NP_001352912.1||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001365984.2|protein_coding|10/10||NM_001365984.2:c.*2122A>C||3846|||||||1||EntrezGene|7788|||||NP_001352913.1||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001365985.2|protein_coding|9/9||NM_001365985.2:c.*2157A>C||3698|||||||1||EntrezGene|7788|||||NP_001352914.1||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001378404.1|protein_coding|11/11||NM_001378404.1:c.*2122A>C||3667|||||||1||EntrezGene|7788|||||NP_001365333.1||||||RefSeq||A|A|||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001378405.1|protein_coding|11/11||NM_001378405.1:c.*2122A>C||3745|||||||1||EntrezGene|7788|YES||||NP_001365334.1||||||RefSeq||A|A|||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_002501.4|protein_coding|10/10||NM_002501.4:c.*2157A>C||3846|||||||1||EntrezGene|7788|||||NP_002492.2||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|LYL1|4066|Transcript|NM_005583.5|protein_coding|||||||||||2262|-1||EntrezGene|6734|YES||||NP_005574.2||||||RefSeq||A|A|||||||||||||||||||||||||||0.77||||||-0.225|0.223|-0.001|-0.001|-13.766|3.716|-10.051|-10.051||||||||;CADD=11.09;CLINVAR_GROUND_TRUTH=Likely_pathogenic;most_severe_consequence=7788:C|3_prime_UTR_variant,6734:C|downstream_gene_variant;Annotation=NFIX,LYL1;VrsModelPrediction=0.01075;VrsModelExplanation=[] GT:DP:AD:GQ 0/0:30:4,26:38 +1 1336445 2052067 A T . . CSQ=T|downstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000344843|protein_coding|||||||||||843|-1||HGNC|14478|YES|||CCDS26.1|ENSP00000341082|RM20_HUMAN||UPI000006F0A8|||Ensembl||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||,T|downstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000482352|protein_coding|||||||||||4044|-1||HGNC|14478|||||ENSP00000460924||B7Z746_HUMAN|UPI00019151C3|||Ensembl||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||,T|downstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000487659|retained_intron|||||||||||848|-1||HGNC|14478|||||||||||Ensembl||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||,T|downstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000492508|protein_coding|||||||||||1117|-1|cds_start_NF|HGNC|14478|||||ENSP00000459994||I3L2X1_HUMAN|UPI00025A2C10|||Ensembl||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||,T|downstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000493287|processed_transcript|||||||||||848|-1||HGNC|14478|||||||||||Ensembl||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||,T|downstream_gene_variant|MODIFIER|MRPL20|55052|Transcript|NM_001318485.2|protein_coding|||||||||||844|-1||EntrezGene|14478|||||NP_001305414.1||||||RefSeq||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||,T|downstream_gene_variant|MODIFIER|MRPL20|55052|Transcript|NM_017971.4|protein_coding|||||||||||844|-1||EntrezGene|14478|YES||||NP_060441.2||||||RefSeq||A|A|||||||||||||||||||||||||||0.00|0.421|||||0.360|0.145|1.604|0.505|-9.975|-0.322|-7.814|-10.297||||||||;CLINVAR_GROUND_TRUTH=Likely_benign;CADD=3.648;most_severe_consequence=14478:T|downstream_gene_variant;Annotation=MRPL20;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;MivmirScore=0.00013;MivmirExplanation=[] GT:DP:AD:GQ 1/1:30:4,26:38 +1 976215 1320032 T G . . CSQ=G|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000379370|protein_coding|4/36||ENST00000379370.2:c.682T>G|ENSP00000368678.2:p.Cys228Gly|732|682|228|C/G|Tgc/Ggc|||1||HGNC|329|YES|||CCDS30551.1|ENSP00000368678|AGRIN_HUMAN|Q5XG79_HUMAN|UPI00001D7C8B|||Ensembl||T|T||deleterious|probably_damaging|Gene3D:3.30.60.30&Pfam:PF07648&PROSITE_profiles:PS51465&PANTHER:PTHR10574&PANTHER:PTHR10574:SF227&SMART:SM00057&SMART:SM00280&Superfamily:SSF100895|||||||3.6|3.6|0.67229|0.347|1.000000|3.561000||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|2.071|8.024|4.707|10.126|-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||,G|non_coding_transcript_exon_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000469403|retained_intron|2/3||ENST00000469403.1:n.629T>G||629|||||||1||HGNC|329|||||||||||Ensembl||T|T||||||||||||||||||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|2.071|8.024|4.707|10.126|-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||,G|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000477585|processed_transcript|||||||||||110|1||HGNC|329|||||||||||Ensembl||T|T||||||||||||||||||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|||||-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||,G|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000479707|retained_intron|||||||||||4564|1||HGNC|329|||||||||||Ensembl||T|T||||||||||||||||||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|||||-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||,G|missense_variant|MODERATE|AGRN|375790|Transcript|NM_001305275.2|protein_coding|4/39||NM_001305275.2:c.682T>G|NP_001292204.1:p.Cys228Gly|735|682|228|C/G|Tgc/Ggc|||1||EntrezGene|329|YES||||NP_001292204.1||||||RefSeq||T|T||deleterious|probably_damaging||||||||3.6|3.6|0.67229|0.347|1.000000|3.561000||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|2.071|8.024|4.707|10.126|-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||,G|missense_variant|MODERATE|AGRN|375790|Transcript|NM_001364727.2|protein_coding|3/36||NM_001364727.2:c.367T>G|NP_001351656.1:p.Cys123Gly|930|367|123|C/G|Tgc/Ggc|||1||EntrezGene|329|||||NP_001351656.1||||||RefSeq||T|T|||||||||||3.6|3.6|0.67229|0.347|1.000000|3.561000||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|2.071|8.024|4.707|10.126|-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||,G|missense_variant|MODERATE|AGRN|375790|Transcript|NM_198576.4|protein_coding|4/36||NM_198576.4:c.682T>G|NP_940978.2:p.Cys228Gly|735|682|228|C/G|Tgc/Ggc|||1||EntrezGene|329|||||NP_940978.2||||||RefSeq||T|T||deleterious|probably_damaging||||||||3.6|3.6|0.67229|0.347|1.000000|3.561000||0|-28|45|-2|0.00|0.00|0.00|0.00|AGRN|0.00|0.421|2.071|8.024|4.707|10.126|-5.576|1.001|-4.574|-4.574|-0.485|-8.504|-8.989|-8.989||||||||;CLINVAR_GROUND_TRUTH=Pathogenic;CADD=26.6;SPIDEX=-1.59;most_severe_consequence=329:G|missense_variant;Annotation=AGRN;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;MivmirScore=0.49679;MivmirExplanation=[] GT:DP:AD:GQ 1/1:30:4,26:38 +2 47403394 1784750 GAGAATGGGGGTGGGGGA TGCCCGCG . . CSQ=TGCCCGCG|intron_variant|MODIFIER|CALM2|ENSG00000143933|Transcript|ENST00000272298|protein_coding||1/5|ENST00000272298.7:c.3+169_3+186delinsCGCGGGCA|||||||||-1||HGNC|1445|YES|||CCDS1832.1|ENSP00000272298|CALM_HUMAN|Q96HY3_HUMAN&G3V361_HUMAN&B4DJ51_HUMAN|UPI00000000C1|||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|9.458|9.219||10.126|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|intron_variant|MODIFIER|CALM2|ENSG00000143933|Transcript|ENST00000409563|protein_coding||1/6|ENST00000409563.1:c.-72+169_-72+186delinsCGCGGGCA|||||||||-1||HGNC|1445|||||ENSP00000387065||Q96HY3_HUMAN&G3V361_HUMAN&E7EMB3_HUMAN|UPI00018815D8|||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|9.458|9.219||10.126|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|intron_variant&NMD_transcript_variant|MODIFIER|CALM2|ENSG00000143933|Transcript|ENST00000432899|nonsense_mediated_decay||1/4|ENST00000432899.1:c.3+169_3+186delinsCGCGGGCA|||||||||-1||HGNC|1445|||||ENSP00000406112||F8WBR5_HUMAN|UPI0001639110|||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|9.458|9.219||10.126|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|intron_variant|MODIFIER|CALM2|ENSG00000143933|Transcript|ENST00000456319|protein_coding||1/6|ENST00000456319.1:c.71+169_71+186delinsCGCGGGCA|||||||||-1|cds_start_NF|HGNC|1445|||||ENSP00000411440||Q96HY3_HUMAN&H0Y7A7_HUMAN&G3V361_HUMAN|UPI00018815D7|||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|8.486|10.998||10.126|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|upstream_gene_variant|MODIFIER|CALM2|ENSG00000143933|Transcript|ENST00000460218|retained_intron|||||||||||2048|-1||HGNC|1445|||||||||||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|||||2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|non_coding_transcript_exon_variant|MODIFIER|CALM2|ENSG00000143933|Transcript|ENST00000484408|processed_transcript|1/6||ENST00000484408.1:n.182_199delinsCGCGGGCA||182-199|||||||-1||HGNC|1445|||||||||||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|8.486|7.434|||2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|splice_donor_5th_base_variant&intron_variant&non_coding_transcript_variant|LOW|CALM2|ENSG00000143933|Transcript|ENST00000489742|processed_transcript||1/4|ENST00000489742.1:n.194+5_194+22delinsCGCGGGCA|||||||||-1||HGNC|1445|||||||||||Ensembl||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|8.486|10.998||3.602|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|intron_variant|MODIFIER|CALM2|805|Transcript|NM_001305624.1|protein_coding||1/6|NM_001305624.1:c.101+169_101+186delinsCGCGGGCA|||||||||-1||EntrezGene|1445|YES||||NP_001292553.1||||||RefSeq||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|OK||||||||||||||||||||||||||0.92|0.124|8.486|10.998||10.126|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|intron_variant|MODIFIER|CALM2|805|Transcript|NM_001305625.2|protein_coding||1/5|NM_001305625.2:c.-106+577_-106+594delinsCGCGGGCA|||||||||-1||EntrezGene|1445|||||NP_001292554.1||||||RefSeq||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|9.458|9.219||7.092|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|upstream_gene_variant|MODIFIER|CALM2|805|Transcript|NM_001305626.1|protein_coding|||||||||||2048|-1||EntrezGene|1445|||||NP_001292555.1||||||RefSeq||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|OK||||||||||||||||||||||||||0.92|0.124|||||2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||,TGCCCGCG|intron_variant|MODIFIER|CALM2|805|Transcript|NM_001743.6|protein_coding||1/5|NM_001743.6:c.3+169_3+186delinsCGCGGGCA|||||||||-1||EntrezGene|1445|||||NP_001734.1||||||RefSeq||GAGAATGGGGGTGGGGGA|GAGAATGGGGGTGGGGGA|||||||||||||||||||||||||||0.92|0.124|9.458|9.219||10.126|2.507|6.864|9.371|9.371|6.459|-2.857|3.602|3.602||||||||;CLINVAR_GROUND_TRUTH=Likely_pathogenic;most_severe_consequence=1445:TGCCCGCG|splice_donor_5th_base_variant;Annotation=CALM2;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;MivmirScore=0.82321;MivmirExplanation=[] GT:DP:AD:GQ 1/1:30:4,26:38 +3 33114704 667634 C T . . CSQ=T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000307363|protein_coding||1/15|ENST00000307363.5:c.76-499G>A|||||||||-1||HGNC|4298|YES|||CCDS43061.1|ENSP00000306920|BGAL_HUMAN|C9JF15_HUMAN&C9J539_HUMAN|UPI0000E5A543|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000307377|protein_coding||1/12|ENST00000307377.8:c.76-499G>A|||||||||-1||HGNC|4298||||CCDS46785.1|ENSP00000305920||F8WF40_HUMAN&E7EQ29_HUMAN|UPI000049DF90|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000399402|protein_coding||1/15|ENST00000399402.3:c.-15-499G>A|||||||||-1||HGNC|4298||||CCDS43062.1|ENSP00000382333|BGAL_HUMAN|C9JF15_HUMAN&C9J539_HUMAN|UPI00015E0895|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||8.418|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000415454|protein_coding||1/5|ENST00000415454.1:c.76-14943G>A|||||||||-1|cds_end_NF|HGNC|4298|||||ENSP00000411813||C9J4G9_HUMAN|UPI000198C9CE|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|11.321|8.077||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000436768|protein_coding||2/3|ENST00000436768.1:c.220-499G>A|||||||||-1|cds_end_NF|HGNC|4298|||||ENSP00000387989||C9JWX1_HUMAN|UPI000198C9CB|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934|6.773|6.745|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000438227|nonsense_mediated_decay||1/4|ENST00000438227.1:c.76-7655G>A|||||||||-1||HGNC|4298|||||ENSP00000401250||F8WEN1_HUMAN|UPI000198C9CD|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|9.360|8.662||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000440656|protein_coding||1/4|ENST00000440656.1:c.-148-4242G>A|||||||||-1|cds_end_NF|HGNC|4298|||||ENSP00000411769||C9J539_HUMAN|UPI000198C9D1|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|9.815|10.126||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000445488|protein_coding||2/16|ENST00000445488.2:c.220-499G>A|||||||||-1||HGNC|4298|||||ENSP00000393377|BGAL_HUMAN|C9JWX1_HUMAN&C9JF15_HUMAN&C9J539_HUMAN|UPI00020654C3|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934|6.773|6.745|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|upstream_gene_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000446732|nonsense_mediated_decay|||||||||||497|-1||HGNC|4298|||||ENSP00000407365||F8WF40_HUMAN|UPI000198C9D0|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|||||-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000450835|protein_coding||2/3|ENST00000450835.1:c.-15-499G>A|||||||||-1|cds_end_NF|HGNC|4298|||||ENSP00000403264||C9JF15_HUMAN|UPI000198C9CC|||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934|6.773|6.745|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000464355|processed_transcript||1/5|ENST00000464355.1:n.34-499G>A|||||||||-1||HGNC|4298|||||||||||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000482097|processed_transcript||1/6|ENST00000482097.1:n.109-19663G>A|||||||||-1||HGNC|4298|||||||||||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.346|8.846||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000485698|processed_transcript||1/5|ENST00000485698.1:n.137-19663G>A|||||||||-1||HGNC|4298|||||||||||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.346|8.846||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|GLB1|ENSG00000170266|Transcript|ENST00000498537|processed_transcript||1/5|ENST00000498537.1:n.133-19663G>A|||||||||-1||HGNC|4298|||||||||||Ensembl||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.346|8.846||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|2720|Transcript|NM_000404.4|protein_coding||1/15|NM_000404.4:c.76-499G>A|||||||||-1||EntrezGene|4298|||||NP_000395.3||||||RefSeq||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|2720|Transcript|NM_001079811.3|protein_coding||1/15|NM_001079811.3:c.-15-499G>A|||||||||-1||EntrezGene|4298|||||NP_001073279.2||||||RefSeq||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||8.418|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|2720|Transcript|NM_001135602.3|protein_coding||1/12|NM_001135602.3:c.76-499G>A|||||||||-1||EntrezGene|4298|||||NP_001129074.2||||||RefSeq||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934||9.930|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||,T|intron_variant|MODIFIER|GLB1|2720|Transcript|NM_001317040.2|protein_coding||2/16|NM_001317040.2:c.220-499G>A|||||||||-1||EntrezGene|4298|YES||||NP_001303969.2||||||RefSeq||C|C||||||||||||||||||-3|-1|17|44|0.00|0.00|0.00|0.00|GLB1|0.00|0.0464|8.856|10.934|6.773|6.745|-2.489|-8.675|-0.850|-11.164|-6.837|-2.838|-9.156|-9.675||||||||;CLINVAR_GROUND_TRUTH=Benign;CADD=2.843;most_severe_consequence=4298:T|intron_variant;Annotation=SUMO2P10,GLB1;MivmirScore=0.00017;MivmirExplanation=[] GT:DP:AD:GQ 0/0:30:4,26:38 +4 1803751 465358 A T . . CSQ=T|missense_variant&splice_region_variant|MODERATE|FGFR3|ENSG00000068078|Transcript|ENST00000260795|protein_coding|6/17||ENST00000260795.2:c.929A>T|ENSP00000260795.2:p.Lys310Met|1031|929|310|K/M|aAg/aTg|||1||HGNC|3690||||CCDS3353.1|ENSP00000260795|FGFR3_HUMAN|Q96T36_HUMAN&Q8NI15_HUMAN|UPI000012A72C|||Ensembl||A|A||deleterious|probably_damaging|Gene3D:2.60.40.10&Pfam:PF07679&PIRSF:PIRSF000628&PROSITE_profiles:PS50835&PANTHER:PTHR24416&PANTHER:PTHR24416:SF128&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726|||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|ENSG00000068078|Transcript|ENST00000340107|protein_coding|7/18||ENST00000340107.4:c.929A>T|ENSP00000339824.4:p.Lys310Met|1185|929|310|K/M|aAg/aTg|||1||HGNC|3690|YES|||CCDS54706.1|ENSP00000339824|FGFR3_HUMAN|Q8NI16_HUMAN|UPI000002A9AC|||Ensembl||A|A||deleterious|probably_damaging|Gene3D:2.60.40.10&Pfam:PF07679&PIRSF:PIRSF000628&PROSITE_profiles:PS50835&PANTHER:PTHR24416&PANTHER:PTHR24416:SF128&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726|||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|11.216|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|ENSG00000068078|Transcript|ENST00000352904|protein_coding|6/15||ENST00000352904.1:c.929A>T|ENSP00000231803.1:p.Lys310Met|968|929|310|K/M|aAg/aTg|||1||HGNC|3690||||CCDS3354.1|ENSP00000231803|FGFR3_HUMAN||UPI000002A9AD|||Ensembl||A|A||deleterious|probably_damaging|PIRSF:PIRSF000628&PANTHER:PTHR24416&PANTHER:PTHR24416:SF128&SMART:SM00409&Superfamily:SSF48726|||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|4.517|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|ENSG00000068078|Transcript|ENST00000412135|protein_coding|7/16||ENST00000412135.2:c.929A>T|ENSP00000412903.2:p.Lys310Met|1185|929|310|K/M|aAg/aTg|||1||HGNC|3690||||CCDS3354.1|ENSP00000412903|FGFR3_HUMAN||UPI000002A9AD|||Ensembl||A|A||deleterious|probably_damaging|PIRSF:PIRSF000628&PANTHER:PTHR24416&PANTHER:PTHR24416:SF128&SMART:SM00409&Superfamily:SSF48726|||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|4.517|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|ENSG00000068078|Transcript|ENST00000440486|protein_coding|7/18||ENST00000440486.2:c.929A>T|ENSP00000414914.2:p.Lys310Met|1185|929|310|K/M|aAg/aTg|||1||HGNC|3690||||CCDS3353.1|ENSP00000414914|FGFR3_HUMAN|Q96T36_HUMAN&Q8NI15_HUMAN|UPI000012A72C|||Ensembl||A|A||deleterious|probably_damaging|Gene3D:2.60.40.10&Pfam:PF07679&PIRSF:PIRSF000628&PROSITE_profiles:PS50835&PANTHER:PTHR24416&PANTHER:PTHR24416:SF128&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726|||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|upstream_gene_variant|MODIFIER|FGFR3|ENSG00000068078|Transcript|ENST00000469068|retained_intron|||||||||||2468|1||HGNC|3690|||||||||||Ensembl||A|A||||||||||||||||||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|||||-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926||||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|FGFR3|ENSG00000068078|Transcript|ENST00000474521|processed_transcript|2/3||ENST00000474521.1:n.305A>T||305|||||||1||HGNC|3690|||||||||||Ensembl||A|A||||||||||||||||||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|11.216|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|ENSG00000068078|Transcript|ENST00000481110|protein_coding|7/17||ENST00000481110.2:c.929A>T|ENSP00000420533.2:p.Lys310Met|1190|929|310|K/M|aAg/aTg|||1||HGNC|3690|||||ENSP00000420533||Q96T36_HUMAN&F8W9L4_HUMAN|UPI00016394EA|||Ensembl||A|A||deleterious|probably_damaging|Gene3D:2.60.40.10&Pfam:PF07679&PROSITE_profiles:PS50835&PANTHER:PTHR24416&PANTHER:PTHR24416:SF128&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726&PIRSF:PIRSF000628|||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|intron_variant|MODIFIER|FGFR3|ENSG00000068078|Transcript|ENST00000507588|protein_coding||3/3|ENST00000507588.1:c.288+101A>T|||||||||1|cds_start_NF&cds_end_NF|HGNC|3690|||||ENSP00000427289||Q96T34_HUMAN|UPI000006D430|||Ensembl||A|A||||||||||||||||||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955||8.067|2.411|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926||||||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|2261|Transcript|NM_000142.5|protein_coding|7/18||NM_000142.5:c.929A>T|NP_000133.1:p.Lys310Met|1204|929|310|K/M|aAg/aTg|||1||EntrezGene|3690|||||NP_000133.1||||||RefSeq||A|A||deleterious|probably_damaging||||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|7/18||NM_001163213.2:c.929A>T|NP_001156685.1:p.Lys310Met|1204|929|310|K/M|aAg/aTg|||1||EntrezGene|3690|YES||||NP_001156685.1||||||RefSeq||A|A||deleterious|probably_damaging||||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|11.216|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|7/18||NM_001354809.2:c.929A>T|NP_001341738.1:p.Lys310Met|1204|929|310|K/M|aAg/aTg|||1||EntrezGene|3690|||||NP_001341738.1||||||RefSeq||A|A|||||||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|7/17||NM_001354810.2:c.929A>T|NP_001341739.1:p.Lys310Met|1204|929|310|K/M|aAg/aTg|||1||EntrezGene|3690|||||NP_001341739.1||||||RefSeq||A|A||deleterious|probably_damaging||||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|10.955|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|missense_variant&splice_region_variant|MODERATE|FGFR3|2261|Transcript|NM_022965.4|protein_coding|7/16||NM_022965.4:c.929A>T|NP_075254.1:p.Lys310Met|1204|929|310|K/M|aAg/aTg|||1||EntrezGene|3690|||||NP_075254.1||||||RefSeq||A|A||deleterious|probably_damaging||||||||4.0|4.0|0.89246|0.698|1.000000|7.207000||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|4.517|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|7/19||NR_148971.2:n.1204A>T||1204|||||||1||EntrezGene|3690|||||||||||RefSeq||A|A||||||||||||||||||1|-38|19|1|0.00|0.00|0.40|0.34|FGFR3|0.00|0.0225|11.216|7.926|8.067|6.745|-1.748|-4.812|3.145|-6.560|4.902|3.024|7.926|7.926|4.902|3.024|7.926|||||;CADD=33;CLINVAR_GROUND_TRUTH=Benign;SPIDEX=-1.441;most_severe_consequence=3690:T|missense_variant;Annotation=FGFR3;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;MivmirScore=0.99434;MivmirExplanation=[CADD=0.28,CSQ_REVEL_score=0.25,GNOMADAF_popmax=0.12,most_severe_consequence=0.09,SWEGENAF=0.09,CSQ_CLINVAR_CLNSIG=0.08,CSQ_SIFT=0.05,CSQ_phyloP100way_vertebrate=0.05,CSQ_SpliceAI_pred_DS_DG=0.03,CSQ_MES-SWA_donor_alt=0.02,Frq=0.02,CSQ_SpliceAI_pred_DS_DL=0.02,CSQ_MES-SWA_donor_diff=0.01,CSQ_SpliceAI_pred_DS_AL=0.00,CSQ_MES-SWA_acceptor_alt=0.00,CSQ_CLINVAR_CLNREVSTAT=0.00,CSQ_SpliceAI_pred_DS_AG=0.00,CSQ_LoFtool=-0.00,CSQ_MaxEntScan_diff=-0.01,CSQ_MaxEntScan_alt=-0.01,CSQ_GERP++_RS=-0.02,CSQ_phastCons100way_vertebrate=-0.02,CSQ_PolyPhen=-0.07,] GT:DP:AD:GQ 1/1:30:4,26:38 +5 45645297 1341556 T G . . CSQ=G|missense_variant|MODERATE|HCN1|ENSG00000164588|Transcript|ENST00000303230|protein_coding|2/8||ENST00000303230.4:c.839A>C|ENSP00000307342.4:p.Gln280Pro|897|839|280|Q/P|cAa/cCa|||-1||HGNC|4845|YES|||CCDS3952.1|ENSP00000307342|HCN1_HUMAN||UPI00001AED69|||Ensembl||T|T||deleterious|benign|Gene3D:1.10.287.70&Pfam:PF00520&PANTHER:PTHR10217&PANTHER:PTHR10217:SF373&Superfamily:SSF81324|||||||5.5|5.5|0.94360|0.821|1.000000|8.017000||20|11|-10|-9|0.00|0.00|0.02|0.00|HCN1|1.00|0.111|8.073|10.065|9.192|10.068|-3.359|-1.672|-5.030|-5.030|-9.949|-0.759|-10.708|-10.708||||||||,G|missense_variant|MODERATE|HCN1|348980|Transcript|NM_021072.4|protein_coding|2/8||NM_021072.4:c.839A>C|NP_066550.2:p.Gln280Pro|1126|839|280|Q/P|cAa/cCa|||-1||EntrezGene|4845|YES||||NP_066550.2||||||RefSeq||T|T||deleterious|benign||||||||5.5|5.5|0.94360|0.821|1.000000|8.017000||20|11|-10|-9|0.00|0.00|0.02|0.00|HCN1|1.00|0.111|8.073|10.065|9.192|10.068|-3.359|-1.672|-5.030|-5.030|-9.949|-0.759|-10.708|-10.708||||||||;CLINVAR_GROUND_TRUTH=Pathogenic;CADD=24;SPIDEX=-0.417;most_severe_consequence=4845:G|missense_variant;Annotation=HCN1;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;MivmirScore=0.97249;MivmirExplanation=[CSQ_REVEL_score=0.42,GNOMADAF_popmax=0.13,CADD=0.12,SWEGENAF=0.11,most_severe_consequence=0.10,CSQ_CLINVAR_CLNSIG=0.09,CSQ_phyloP100way_vertebrate=0.04,CSQ_SIFT=0.04,Frq=0.02,CSQ_MES-SWA_acceptor_alt=0.00,CSQ_SpliceAI_pred_DS_AG=0.00,CSQ_SpliceAI_pred_DS_AL=0.00,CSQ_MES-SWA_donor_diff=0.00,CSQ_MES-SWA_donor_alt=0.00,CSQ_LoFtool=0.00,CSQ_MaxEntScan_diff=0.00,CSQ_MaxEntScan_alt=0.00,CSQ_SpliceAI_pred_DS_DG=0.00,CSQ_SpliceAI_pred_DS_DL=-0.01,CSQ_GERP++_RS=-0.01,CSQ_CLINVAR_CLNREVSTAT=-0.02,CSQ_phastCons100way_vertebrate=-0.02,CSQ_PolyPhen=-0.06,] GT:DP:AD:GQ 1/1:30:4,26:38 +5 45645306 635188 T C . . CSQ=C|missense_variant|MODERATE|HCN1|ENSG00000164588|Transcript|ENST00000303230|protein_coding|2/8||ENST00000303230.4:c.830A>G|ENSP00000307342.4:p.Tyr277Cys|888|830|277|Y/C|tAc/tGc|||-1||HGNC|4845|YES|||CCDS3952.1|ENSP00000307342|HCN1_HUMAN||UPI00001AED69|||Ensembl||T|T||deleterious|probably_damaging|Gene3D:1.10.287.70&Pfam:PF00520&PANTHER:PTHR10217&PANTHER:PTHR10217:SF373&Superfamily:SSF81324|||||||5.5|5.5|0.99415|0.961|1.000000|8.017000||11|-19|-19|12|0.00|0.00|0.05|0.00|HCN1|1.00|0.111|8.073|10.065|9.192|10.068|-2.879|-0.050|-2.929|-2.929|-7.371|3.551|-3.820|-3.820||||||||,C|missense_variant|MODERATE|HCN1|348980|Transcript|NM_021072.4|protein_coding|2/8||NM_021072.4:c.830A>G|NP_066550.2:p.Tyr277Cys|1117|830|277|Y/C|tAc/tGc|||-1||EntrezGene|4845|YES||||NP_066550.2||||||RefSeq||T|T||deleterious|probably_damaging||||||||5.5|5.5|0.99415|0.961|1.000000|8.017000||11|-19|-19|12|0.00|0.00|0.05|0.00|HCN1|1.00|0.111|8.073|10.065|9.192|10.068|-2.879|-0.050|-2.929|-2.929|-7.371|3.551|-3.820|-3.820||||||||;CLINVAR_GROUND_TRUTH=Pathogenic;CADD=29.2;SPIDEX=0.253;most_severe_consequence=4845:C|missense_variant;Annotation=HCN1;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;MivmirScore=0.99276;MivmirExplanation=[CSQ_REVEL_score=0.41,CADD=0.15,GNOMADAF_popmax=0.13,most_severe_consequence=0.11,SWEGENAF=0.11,CSQ_CLINVAR_CLNSIG=0.08,CSQ_SIFT=0.05,CSQ_phyloP100way_vertebrate=0.04,Frq=0.02,CSQ_SpliceAI_pred_DS_AG=0.01,CSQ_MaxEntScan_alt=0.00,CSQ_SpliceAI_pred_DS_AL=0.00,CSQ_SpliceAI_pred_DS_DG=0.00,CSQ_MES-SWA_donor_diff=0.00,CSQ_LoFtool=0.00,CSQ_MES-SWA_acceptor_alt=0.00,CSQ_MaxEntScan_diff=0.00,CSQ_SpliceAI_pred_DS_DL=-0.00,CSQ_MES-SWA_donor_alt=-0.01,CSQ_CLINVAR_CLNREVSTAT=-0.01,CSQ_phastCons100way_vertebrate=-0.02,CSQ_GERP++_RS=-0.02,CSQ_PolyPhen=-0.06,] GT:DP:AD:GQ 1/1:30:4,26:38 +6 7580872 1072470 A ACT . . CSQ=CT|frameshift_variant|HIGH|DSP|ENSG00000096696|Transcript|ENST00000379802|protein_coding|23/24||ENST00000379802.3:c.4449_4450insCT|ENSP00000369129.3:p.Glu1484LeufsTer4|4790-4791|4449-4450|1483-1484|-/X|-/CT|||1||HGNC|3052|YES|||CCDS4501.1|ENSP00000369129|DESP_HUMAN|G1UI31_HUMAN&B4DKX6_HUMAN|UPI000013C67F|||Ensembl|||||||Coiled-coils_(Ncoils):Coil&PANTHER:PTHR11915:SF234&PANTHER:PTHR11915|||||||||||||||||||||||1.00|0.077|10.540|6.347|9.971|8.829|-9.260|-1.245|-10.504|-10.504|-0.510|-3.129|-3.639|-3.639||||||||,CT|intron_variant|MODIFIER|DSP|ENSG00000096696|Transcript|ENST00000418664|protein_coding||23/23|ENST00000418664.2:c.3582+867_3582+868insCT|||||||||1||HGNC|3052||||CCDS47368.1|ENSP00000396591|DESP_HUMAN|Q4LE79_HUMAN&G1UI31_HUMAN&B4DKX6_HUMAN|UPI00004C9B0E|||Ensembl||||||||||||||||||||||||||||||1.00|0.077|10.540||9.971|10.567|-9.260|-1.245|-10.504|-10.504|-0.510|-3.129|-3.639|-3.639||||||||,CT|intron_variant|MODIFIER|DSP|1832|Transcript|NM_001008844.3|protein_coding||23/23|NM_001008844.3:c.3582+867_3582+868insCT|||||||||1||EntrezGene|3052|||||NP_001008844.1||||||RefSeq||||OK||||||||||||||||||||||||||1.00|0.077|10.540||9.971|10.567|-9.260|-1.245|-10.504|-10.504|-0.510|-3.129|-3.639|-3.639||||||||,CT|intron_variant|MODIFIER|DSP|1832|Transcript|NM_001319034.2|protein_coding||23/23|NM_001319034.2:c.4050+399_4050+400insCT|||||||||1||EntrezGene|3052|||||NP_001305963.1||||||RefSeq||||OK||||||||||||||||||||||||||1.00|0.077|10.540||9.971|10.567|-9.260|-1.245|-10.504|-10.504|-0.510|-3.129|-3.639|-3.639||||||||,CT|frameshift_variant|HIGH|DSP|1832|Transcript|NM_004415.4|protein_coding|23/24||NM_004415.4:c.4449_4450insCT|NP_004406.2:p.Glu1484LeufsTer4|4694-4695|4449-4450|1483-1484|-/X|-/CT|||1||EntrezGene|3052|YES||||NP_004406.2||||||RefSeq||||OK||||||||||||||||||||||||||1.00|0.077|10.540|6.347|9.971|8.829|-9.260|-1.245|-10.504|-10.504|-0.510|-3.129|-3.639|-3.639||||||||;CADD=33;CLINVAR_GROUND_TRUTH=Pathogenic;most_severe_consequence=3052:CT|frameshift_variant;Annotation=DSP;MivmirScore=0.99743;MivmirExplanation=[most_severe_consequence=0.39,CADD=0.27,GNOMADAF_popmax=0.13,SWEGENAF=0.10,CSQ_CLINVAR_CLNSIG=0.10,Frq=0.01,CSQ_MES-SWA_acceptor_alt=0.01,CSQ_SpliceAI_pred_DS_AG=0.00,CSQ_MaxEntScan_alt=0.00,CSQ_MES-SWA_donor_alt=0.00,CSQ_SIFT=0.00,CSQ_PolyPhen=0.00,CSQ_phyloP100way_vertebrate=0.00,CSQ_MaxEntScan_diff=0.00,CSQ_phastCons100way_vertebrate=0.00,CSQ_LoFtool=0.00,CSQ_GERP++_RS=0.00,CSQ_REVEL_score=0.00,CSQ_SpliceAI_pred_DS_DL=0.00,CSQ_SpliceAI_pred_DS_AL=0.00,CSQ_MES-SWA_donor_diff=0.00,CSQ_SpliceAI_pred_DS_DG=0.00,CSQ_CLINVAR_CLNREVSTAT=-0.02,] GT:DP:AD:GQ 0/0:30:4,26:38 +6 7580957 923905 T C . . CSQ=C|missense_variant|MODERATE|DSP|ENSG00000096696|Transcript|ENST00000379802|protein_coding|23/24||ENST00000379802.3:c.4534T>C|ENSP00000369129.3:p.Tyr1512His|4875|4534|1512|Y/H|Tat/Cat|||1||HGNC|3052|YES|||CCDS4501.1|ENSP00000369129|DESP_HUMAN|G1UI31_HUMAN&B4DKX6_HUMAN|UPI000013C67F|||Ensembl||T|T||tolerated|possibly_damaging|Coiled-coils_(Ncoils):Coil&PANTHER:PTHR11915:SF234&PANTHER:PTHR11915|||||||5.74|3.3|0.21181|0.071|0.260000|0.431000|rs779987722|-29|23|21|-7|0.00|0.00|0.00|0.00|DSP|1.00|0.077|10.540|6.347|9.971|8.829|0.598|0.309|0.907|0.907|-5.393|7.754|2.361|2.361||||||||,C|intron_variant|MODIFIER|DSP|ENSG00000096696|Transcript|ENST00000418664|protein_coding||23/23|ENST00000418664.2:c.3582+952T>C|||||||||1||HGNC|3052||||CCDS47368.1|ENSP00000396591|DESP_HUMAN|Q4LE79_HUMAN&G1UI31_HUMAN&B4DKX6_HUMAN|UPI00004C9B0E|||Ensembl||T|T||||||||||||||||||-29|23|21|-7|0.00|0.00|0.00|0.00|DSP|1.00|0.077|10.540||9.971|10.567|0.598|0.309|0.907|0.907|-5.393|7.754|2.361|2.361||||||||,C|intron_variant|MODIFIER|DSP|1832|Transcript|NM_001008844.3|protein_coding||23/23|NM_001008844.3:c.3582+952T>C|||||||||1||EntrezGene|3052|||||NP_001008844.1||||||RefSeq||T|T|OK|||||||||||||||||-29|23|21|-7|0.00|0.00|0.00|0.00|DSP|1.00|0.077|10.540||9.971|10.567|0.598|0.309|0.907|0.907|-5.393|7.754|2.361|2.361||||||||,C|intron_variant|MODIFIER|DSP|1832|Transcript|NM_001319034.2|protein_coding||23/23|NM_001319034.2:c.4050+484T>C|||||||||1||EntrezGene|3052|||||NP_001305963.1||||||RefSeq||T|T|OK|||||||||||||||||-29|23|21|-7|0.00|0.00|0.00|0.00|DSP|1.00|0.077|10.540||9.971|10.567|0.598|0.309|0.907|0.907|-5.393|7.754|2.361|2.361||||||||,C|missense_variant|MODERATE|DSP|1832|Transcript|NM_004415.4|protein_coding|23/24||NM_004415.4:c.4534T>C|NP_004406.2:p.Tyr1512His|4779|4534|1512|Y/H|Tat/Cat|||1||EntrezGene|3052|YES||||NP_004406.2||||||RefSeq||T|T|OK|tolerated|possibly_damaging||||||||5.74|3.3|0.21181|0.071|0.260000|0.431000|rs779987722|-29|23|21|-7|0.00|0.00|0.00|0.00|DSP|1.00|0.077|10.540|6.347|9.971|8.829|0.598|0.309|0.907|0.907|-5.393|7.754|2.361|2.361||||||||;SPIDEX=-0.068;CADD=15.86;CLINVAR_GROUND_TRUTH=Benign/Likely_benign;most_severe_consequence=3052:C|missense_variant;Annotation=DSP;MivmirScore=0.05780;MivmirExplanation=[] GT:DP:AD:GQ 0/0:30:4,26:38 +7 50458565 360425 T G . . CSQ=G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000331340|protein_coding||6/7|ENST00000331340.3:c.716-862T>G|||||||||1||HGNC|13176|||||ENSP00000331614|IKZF1_HUMAN||UPI000012D465|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000343574|protein_coding||5/6|ENST00000343574.5:c.455-862T>G|||||||||1||HGNC|13176|||||ENSP00000342750|IKZF1_HUMAN||UPI000002ABB9|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000346667|protein_coding||3/3|ENST00000346667.4:c.161-9051T>G|||||||||1||HGNC|13176|||||ENSP00000340080|IKZF1_HUMAN|Q3T907_HUMAN|UPI000002ABBD|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.743|10.239|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000349824|protein_coding||4/4|ENST00000349824.4:c.422-9051T>G|||||||||1||HGNC|13176||||CCDS69299.1|ENSP00000342485|IKZF1_HUMAN||UPI000002ABBC|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||8.553|9.675|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000357364|protein_coding||5/5|ENST00000357364.4:c.589+8160T>G|||||||||1||HGNC|13176|||||ENSP00000349928|IKZF1_HUMAN||UPI000002ABBA|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000359197|protein_coding||5/6|ENST00000359197.5:c.590-862T>G|||||||||1||HGNC|13176||||CCDS59055.1|ENSP00000352123|IKZF1_HUMAN||UPI000002ABBE|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000426121|protein_coding||1/1|ENST00000426121.1:c.110-9051T>G|||||||||1|cds_start_NF&cds_end_NF|HGNC|13176|||||ENSP00000409588||Q3T907_HUMAN|UPI00005B2C77|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010|||10.239|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000438033|protein_coding||5/6|ENST00000438033.1:c.455-862T>G|||||||||1||HGNC|13176|||||ENSP00000396554|IKZF1_HUMAN||UPI000002ABB9|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000439701|protein_coding||5/6|ENST00000439701.1:c.590-862T>G|||||||||1||HGNC|13176|YES|||CCDS59055.1|ENSP00000413025|IKZF1_HUMAN||UPI000002ABBE|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000440768|protein_coding||5/7|ENST00000440768.2:c.590-862T>G|||||||||1||HGNC|13176|||||ENSP00000401507|IKZF1_HUMAN||UPI0000401AEF|||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|-5.489|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000471793|retained_intron||4/5|ENST00000471793.1:n.935-862T>G|||||||||1||HGNC|13176|||||||||||Ensembl||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220765.3|protein_coding||5/6|NM_001220765.3:c.590-862T>G|||||||||1||EntrezGene|13176|||||NP_001207694.1||||||RefSeq||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220767.2|protein_coding||4/5|NM_001220767.2:c.455-862T>G|||||||||1||EntrezGene|13176|||||NP_001207696.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|7.688|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220768.2|protein_coding||4/4|NM_001220768.2:c.589+8160T>G|||||||||1||EntrezGene|13176|||||NP_001207697.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220770.2|protein_coding||3/4|NM_001220770.2:c.329-862T>G|||||||||1||EntrezGene|13176|||||NP_001207699.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|7.688|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220771.2|protein_coding||3/3|NM_001220771.2:c.422-9051T>G|||||||||1||EntrezGene|13176|||||NP_001207700.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||8.553|9.675|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291837.2|protein_coding||5/6|NM_001291837.2:c.590-862T>G|||||||||1||EntrezGene|13176|||||NP_001278766.1||||||RefSeq||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291838.2|protein_coding||5/6|NM_001291838.2:c.455-862T>G|||||||||1||EntrezGene|13176|||||NP_001278767.1||||||RefSeq||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291839.2|protein_coding||4/5|NM_001291839.2:c.329-862T>G|||||||||1||EntrezGene|13176|||||NP_001278768.1||||||RefSeq||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|9.944|9.394|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291840.1|protein_coding||2/2|NM_001291840.1:c.161-9051T>G|||||||||1||EntrezGene|13176|||||NP_001278769.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.743|10.239|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291841.1|protein_coding||3/4|NM_001291841.1:c.287-862T>G|||||||||1||EntrezGene|13176|||||NP_001278770.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291842.1|protein_coding||3/4|NM_001291842.1:c.287-862T>G|||||||||1||EntrezGene|13176|||||NP_001278771.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|7.688|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291843.1|protein_coding||2/3|NM_001291843.1:c.161-862T>G|||||||||1||EntrezGene|13176|||||NP_001278772.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|9.743|10.239|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291844.1|protein_coding||2/3|NM_001291844.1:c.161-862T>G|||||||||1||EntrezGene|13176|||||NP_001278773.1||||||RefSeq||T|T|OK|||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|7.688|9.743|10.239|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_006060.6|protein_coding||6/7|NM_006060.6:c.716-862T>G|||||||||1||EntrezGene|13176|YES||||NP_006051.1||||||RefSeq||T|T||||||||||||||||||44|23|44|-6|0.00|0.00|0.00|0.00|IKZF1|1.00||7.939|8.846|8.187|9.884|-3.420|1.323|-2.097|-2.097|-2.791|1.016|-1.775|-1.775||||||||;CADD=3.134;CLINVAR_GROUND_TRUTH=Benign;most_severe_consequence=13176:G|intron_variant;Annotation=IKZF1;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;MivmirScore=0.00017;MivmirExplanation=[] GT:DP:AD:GQ 1/1:30:4,26:38 +7 50463289 2136536 C G . . CSQ=G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000331340|protein_coding||7/7|ENST00000331340.3:c.850+3728C>G|||||||||1||HGNC|13176|||||ENSP00000331614|IKZF1_HUMAN||UPI000012D465|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000343574|protein_coding||6/6|ENST00000343574.5:c.589+3728C>G|||||||||1||HGNC|13176|||||ENSP00000342750|IKZF1_HUMAN||UPI000002ABB9|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000346667|protein_coding||3/3|ENST00000346667.4:c.161-4327C>G|||||||||1||HGNC|13176|||||ENSP00000340080|IKZF1_HUMAN|Q3T907_HUMAN|UPI000002ABBD|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.743|10.239|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000349824|protein_coding||4/4|ENST00000349824.4:c.422-4327C>G|||||||||1||HGNC|13176||||CCDS69299.1|ENSP00000342485|IKZF1_HUMAN||UPI000002ABBC|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||8.553|9.675|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000357364|protein_coding||5/5|ENST00000357364.4:c.590-4327C>G|||||||||1||HGNC|13176|||||ENSP00000349928|IKZF1_HUMAN||UPI000002ABBA|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.944|9.394|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000359197|protein_coding||6/6|ENST00000359197.5:c.724+3728C>G|||||||||1||HGNC|13176||||CCDS59055.1|ENSP00000352123|IKZF1_HUMAN||UPI000002ABBE|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000426121|protein_coding||1/1|ENST00000426121.1:c.110-4327C>G|||||||||1|cds_start_NF&cds_end_NF|HGNC|13176|||||ENSP00000409588||Q3T907_HUMAN|UPI00005B2C77|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010|||10.239|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000438033|protein_coding||6/6|ENST00000438033.1:c.589+3728C>G|||||||||1||HGNC|13176|||||ENSP00000396554|IKZF1_HUMAN||UPI000002ABB9|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000439701|protein_coding||6/6|ENST00000439701.1:c.724+3728C>G|||||||||1||HGNC|13176|YES|||CCDS59055.1|ENSP00000413025|IKZF1_HUMAN||UPI000002ABBE|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000440768|protein_coding||7/7|ENST00000440768.2:c.*41+3728C>G|||||||||1||HGNC|13176|||||ENSP00000401507|IKZF1_HUMAN||UPI0000401AEF|||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||-29.410|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|IKZF1|ENSG00000185811|Transcript|ENST00000471793|retained_intron||5/5|ENST00000471793.1:n.1069+3728C>G|||||||||1||HGNC|13176|||||||||||Ensembl||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220765.3|protein_coding||6/6|NM_001220765.3:c.724+3728C>G|||||||||1||EntrezGene|13176|||||NP_001207694.1||||||RefSeq||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220767.2|protein_coding||5/5|NM_001220767.2:c.559+3758C>G|||||||||1||EntrezGene|13176|||||NP_001207696.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|7.688|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220768.2|protein_coding||4/4|NM_001220768.2:c.590-4327C>G|||||||||1||EntrezGene|13176|||||NP_001207697.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.944|9.394|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220770.2|protein_coding||4/4|NM_001220770.2:c.433+3758C>G|||||||||1||EntrezGene|13176|||||NP_001207699.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|7.688|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001220771.2|protein_coding||3/3|NM_001220771.2:c.422-4327C>G|||||||||1||EntrezGene|13176|||||NP_001207700.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||8.553|9.675|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291837.2|protein_coding||6/6|NM_001291837.2:c.724+3728C>G|||||||||1||EntrezGene|13176|||||NP_001278766.1||||||RefSeq||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291838.2|protein_coding||6/6|NM_001291838.2:c.589+3728C>G|||||||||1||EntrezGene|13176|||||NP_001278767.1||||||RefSeq||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291839.2|protein_coding||5/5|NM_001291839.2:c.463+3728C>G|||||||||1||EntrezGene|13176|||||NP_001278768.1||||||RefSeq||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291840.1|protein_coding||2/2|NM_001291840.1:c.161-4327C>G|||||||||1||EntrezGene|13176|||||NP_001278769.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||9.743|10.239|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291841.1|protein_coding||4/4|NM_001291841.1:c.421+3728C>G|||||||||1||EntrezGene|13176|||||NP_001278770.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291842.1|protein_coding||4/4|NM_001291842.1:c.391+3758C>G|||||||||1||EntrezGene|13176|||||NP_001278771.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|7.688|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291843.1|protein_coding||3/3|NM_001291843.1:c.295+3728C>G|||||||||1||EntrezGene|13176|||||NP_001278772.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_001291844.1|protein_coding||3/3|NM_001291844.1:c.265+3758C>G|||||||||1||EntrezGene|13176|||||NP_001278773.1||||||RefSeq||C|C|OK|||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|7.688|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||,G|intron_variant|MODIFIER|IKZF1|10320|Transcript|NM_006060.6|protein_coding||7/7|NM_006060.6:c.850+3728C>G|||||||||1||EntrezGene|13176|YES||||NP_006051.1||||||RefSeq||C|C||||||||||||||||||-12|-21|-40|-9|0.00|0.00|0.00|0.00|IKZF1|1.00||10.010||7.939|8.846|-4.897|0.255|-2.593|-4.642|-15.344|-8.651|-16.814|-23.995||||||||;CADD=4.931;CLINVAR_GROUND_TRUTH=Pathogenic;most_severe_consequence=13176:G|intron_variant;Annotation=IKZF1;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;MivmirScore=0.00023;MivmirExplanation=[] GT:DP:AD:GQ 1/1:30:4,26:38 +9 13193319 1657520 A AG . . CSQ=G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000319217|protein_coding||13/46|ENST00000319217.7:c.1657-8dup|||||||||-1||HGNC|7208|||||ENSP00000320006|MPDZ_HUMAN|B3KRN5_HUMAN&B3KQC9_HUMAN|UPI0000211133|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000381015|protein_coding||12/45|ENST00000381015.4:c.1657-8dup|||||||||-1||HGNC|7208|||||ENSP00000370403|MPDZ_HUMAN|B3KRN5_HUMAN&B3KQC9_HUMAN|UPI0000211133|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000381022|protein_coding||12/44|ENST00000381022.2:c.1657-8dup|||||||||-1||HGNC|7208||||CCDS47951.1|ENSP00000370410|MPDZ_HUMAN||UPI00015367D3|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000447879|protein_coding||12/44|ENST00000447879.1:c.1657-8dup|||||||||-1||HGNC|7208||||CCDS59120.1|ENSP00000415208|MPDZ_HUMAN|B7ZB24_HUMAN&B3KRN5_HUMAN&B3KQC9_HUMAN|UPI0000151582|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000536827|protein_coding||12/43|ENST00000536827.1:c.1657-8dup|||||||||-1||HGNC|7208||||CCDS59119.1|ENSP00000444151|MPDZ_HUMAN||UPI000191706B|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|upstream_gene_variant|MODIFIER|MPDZ|ENSG00000107186|Transcript|ENST00000539508|retained_intron|||||||||||3143|-1||HGNC|7208|||||||||||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|||||14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000541718|protein_coding||13/45|ENST00000541718.1:c.1657-8dup|||||||||-1||HGNC|7208|YES|||CCDS47951.1|ENSP00000439807|MPDZ_HUMAN||UPI00015367D3|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|ENSG00000107186|Transcript|ENST00000546205|protein_coding||13/47|ENST00000546205.1:c.1657-8dup|||||||||-1||HGNC|7208|||||ENSP00000446358||F5H1U9_HUMAN&B3KRN5_HUMAN&B3KQC9_HUMAN|UPI000204A742|||Ensembl|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001261406.2|protein_coding||13/45|NM_001261406.2:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001248335.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001261407.2|protein_coding||13/44|NM_001261407.2:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001248336.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001330637.2|protein_coding||13/46|NM_001330637.2:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001317566.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375413.1|protein_coding||13/47|NM_001375413.1:c.1657-8dup|||||||||-1||EntrezGene|7208|YES||||NP_001362342.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375416.1|protein_coding||13/45|NM_001375416.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362345.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375417.1|protein_coding||13/45|NM_001375417.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362346.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375418.1|protein_coding||14/46|NM_001375418.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362347.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375419.1|protein_coding||13/44|NM_001375419.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362348.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375420.1|protein_coding||13/44|NM_001375420.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362349.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375421.1|protein_coding||14/45|NM_001375421.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362350.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375422.1|protein_coding||13/44|NM_001375422.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362351.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375423.1|protein_coding||14/45|NM_001375423.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362352.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375424.1|protein_coding||13/44|NM_001375424.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362353.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375425.1|protein_coding||13/43|NM_001375425.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362354.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375426.1|protein_coding||13/43|NM_001375426.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362355.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001375427.1|protein_coding||13/42|NM_001375427.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001362356.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_001378778.1|protein_coding||13/46|NM_001378778.1:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_001365707.1||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MPDZ|8777|Transcript|NM_003829.5|protein_coding||13/45|NM_003829.5:c.1657-8dup|||||||||-1||EntrezGene|7208|||||NP_003820.2||||||RefSeq|||||||||||||||||||||-8|-31|-24|-16|0.00|0.00|0.00|0.00|MPDZ|0.00|0.998|14.026|6.381|8.505|7.229|14.879|-0.853|14.026|14.026|-13.828|0.000|-13.828|-13.828||||||||;CLINVAR_GROUND_TRUTH=Benign;CADD=6.052;most_severe_consequence=7208:G|splice_region_variant;Annotation=MPDZ;GeneticModels=clinvar:AR_hom;ModelScore=clinvar:38;MivmirScore=0.00437;MivmirExplanation=[] GT:DP:AD:GQ 1/1:30:4,26:38 +19 13207585 1172824 A C . . CSQ=C|downstream_gene_variant|MODIFIER|LYL1|ENSG00000104903|Transcript|ENST00000264824|protein_coding|||||||||||2262|-1||HGNC|6734|YES|||CCDS12292.1|ENSP00000264824|LYL1_HUMAN|K7ER61_HUMAN|UPI000013D576|||Ensembl||A|A|||||||||||||||||||||||||||0.77||||||-0.225|0.223|-0.001|-0.001|-13.766|3.716|-10.051|-10.051||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000358552|protein_coding|9/9||ENST00000358552.3:c.*2122A>C||3505|||||||1||HGNC|7788|||||ENSP00000351354||K7ESG9_HUMAN&K7EKH0_HUMAN&C9JWJ8_HUMAN|UPI0000456C1A|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000360105|protein_coding|9/9||ENST00000360105.4:c.*2157A>C||3434|||||||1||HGNC|7788|||||ENSP00000353219||K7ESG9_HUMAN&K7EKH0_HUMAN|UPI0000366D41|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000397661|protein_coding|||||||||||570|1||HGNC|7788|YES|||CCDS45996.1|ENSP00000380781|NFIX_HUMAN|K7ESG9_HUMAN&K7EKH0_HUMAN|UPI000002AF1D|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000585575|protein_coding|||||||||||2122|1||HGNC|7788|||||ENSP00000468794|NFIX_HUMAN|K7ESG9_HUMAN&K7EN08_HUMAN&K7EKH0_HUMAN&D2DXM9_HUMAN|UPI000002AF1E|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000586797|nonsense_mediated_decay|||||||||||2087|1||HGNC|7788|||||ENSP00000467536||K7EPU2_HUMAN|UPI0002840A61|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000587260|protein_coding|||||||||||2001|1||HGNC|7788|||||ENSP00000467785|NFIX_HUMAN|K7ESG9_HUMAN&K7EKH0_HUMAN|UPI000002AF1F|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000587760|protein_coding|||||||||||2013|1||HGNC|7788||||CCDS59359.1|ENSP00000466389|NFIX_HUMAN|K7ESG9_HUMAN&K7EKH0_HUMAN|UPI000003B460|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000588228|protein_coding|||||||||||2016|1||HGNC|7788|||||ENSP00000466735||K7ESG9_HUMAN&K7EN08_HUMAN&K7EKH0_HUMAN|UPI00006DE7B6|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|LYL1|ENSG00000104903|Transcript|ENST00000590120|retained_intron|||||||||||4407|-1||HGNC|6734|||||||||||Ensembl||A|A|||||||||||||||||||||||||||0.77||||||-0.225|0.223|-0.001|-0.001|-13.766|3.716|-10.051|-10.051||||||||,C|downstream_gene_variant|MODIFIER|LYL1|ENSG00000104903|Transcript|ENST00000590974|protein_coding|||||||||||3919|-1|cds_end_NF|HGNC|6734|||||ENSP00000468122||K7ER61_HUMAN|UPI0002840A94|||Ensembl||A|A|||||||||||||||||||||||||||0.77||||||-0.225|0.223|-0.001|-0.001|-13.766|3.716|-10.051|-10.051||||||||,C|downstream_gene_variant|MODIFIER|NFIX|ENSG00000008441|Transcript|ENST00000592199|protein_coding|||||||||||2122|1||HGNC|7788|||||ENSP00000467512|NFIX_HUMAN|K7ESG9_HUMAN&K7EN08_HUMAN&K7EKH0_HUMAN|UPI000012FFCC|||Ensembl||A|A|||||||||||||||||||||||||||1.00|0.0911|||||3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001271043.2|protein_coding|11/11||NM_001271043.2:c.*2122A>C||3708|||||||1||EntrezGene|7788|||||NP_001257972.1||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001271044.3|protein_coding|10/10||NM_001271044.3:c.*2157A>C||3519|||||||1||EntrezGene|7788|||||NP_001257973.1||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001365902.3|protein_coding|11/11||NM_001365902.3:c.*2122A>C||3994|||||||1||EntrezGene|7788|||||NP_001352831.1||||||RefSeq||A|A|||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001365982.2|protein_coding|9/9||NM_001365982.2:c.*2157A>C||3723|||||||1||EntrezGene|7788|||||NP_001352911.1||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001365983.2|protein_coding|10/10||NM_001365983.2:c.*2157A>C||3560|||||||1||EntrezGene|7788|||||NP_001352912.1||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001365984.2|protein_coding|10/10||NM_001365984.2:c.*2122A>C||3846|||||||1||EntrezGene|7788|||||NP_001352913.1||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001365985.2|protein_coding|9/9||NM_001365985.2:c.*2157A>C||3698|||||||1||EntrezGene|7788|||||NP_001352914.1||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001378404.1|protein_coding|11/11||NM_001378404.1:c.*2122A>C||3667|||||||1||EntrezGene|7788|||||NP_001365333.1||||||RefSeq||A|A|||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_001378405.1|protein_coding|11/11||NM_001378405.1:c.*2122A>C||3745|||||||1||EntrezGene|7788|YES||||NP_001365334.1||||||RefSeq||A|A|||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|3_prime_UTR_variant|MODIFIER|NFIX|4784|Transcript|NM_002501.4|protein_coding|10/10||NM_002501.4:c.*2157A>C||3846|||||||1||EntrezGene|7788|||||NP_002492.2||||||RefSeq||A|A|OK||||||||||||||||||||||||||1.00|0.0911|||9.894|9.786|3.073|-5.260|-2.187|-2.187|-1.204|-2.388|-0.459|-3.591||||||||,C|downstream_gene_variant|MODIFIER|LYL1|4066|Transcript|NM_005583.5|protein_coding|||||||||||2262|-1||EntrezGene|6734|YES||||NP_005574.2||||||RefSeq||A|A|||||||||||||||||||||||||||0.77||||||-0.225|0.223|-0.001|-0.001|-13.766|3.716|-10.051|-10.051||||||||;CADD=11.09;CLINVAR_GROUND_TRUTH=Likely_pathogenic;most_severe_consequence=7788:C|3_prime_UTR_variant,6734:C|downstream_gene_variant;Annotation=NFIX,LYL1;MivmirScore=0.01075;MivmirExplanation=[] GT:DP:AD:GQ 0/0:30:4,26:38 diff --git a/src/tests/variant_rank_score/test_inference.py b/src/tests/variant_rank_score/test_inference.py index 8ece1a3c..4d4a8f04 100644 --- a/src/tests/variant_rank_score/test_inference.py +++ b/src/tests/variant_rank_score/test_inference.py @@ -16,8 +16,8 @@ def parse_vrs_explanations(explanation: str) -> dict: """ - Parse VrsModelExplanation field - :param explanation: INFO key field contents for VrsModelExplanation + Parse MivmirExplanation field + :param explanation: INFO key field contents for MivmirExplanation :return: Parsed dict, parts in explanation split into dict content """ # @@ -144,14 +144,14 @@ def test_inference(work_dir, n_cores): variant.POS == variant_ref.POS: # Test model inference # Model prediction comes with a precision of 5 decimal points (rest is just noise in comparison) - assert isclose(variant.INFO['VrsModelPrediction'], - variant_ref.INFO['VrsModelPrediction'], - atol=1E-5), (variant.INFO['VrsModelPrediction'], - variant_ref.INFO['VrsModelPrediction'], + assert isclose(variant.INFO['MivmirScore'], + variant_ref.INFO['MivmirScore'], + atol=1E-5), (variant.INFO['MivmirScore'], + variant_ref.INFO['MivmirScore'], variant.ID, variant_ref.ID) # Test model explanations - explanation = parse_vrs_explanations(variant.INFO['VrsModelExplanation']) - explanation_ref = parse_vrs_explanations(variant_ref.INFO['VrsModelExplanation']) + explanation = parse_vrs_explanations(variant.INFO['MivmirExplanation']) + explanation_ref = parse_vrs_explanations(variant_ref.INFO['MivmirExplanation']) if len(explanation_ref) > 0: # Model explanations comes with a precision of 2 decimal points for key in explanation_ref.keys(): @@ -214,4 +214,3 @@ def test_inference_batch_composition(ignore_clinvar_uncertain_conflicting_annota d = d.dropna() err = np.sum(np.abs(d.values)) assert np.isclose(err, 0.0, atol=1E-3), (column, d) - From c40897487a3c40d9378ce4a1fda54bf043171cb9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tor=20Bj=C3=B6rgen?= Date: Mon, 8 Dec 2025 15:27:13 +0100 Subject: [PATCH 2/2] GICAM: Change VCF inference key from 'GICAM' -> 'GicamScore' MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Tor Björgen --- src/rdds/gicam/vcf_inference/infer_vcf.py | 6 +++--- src/tests/gicam/test_inference.py | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/rdds/gicam/vcf_inference/infer_vcf.py b/src/rdds/gicam/vcf_inference/infer_vcf.py index de40c76d..9897c8f4 100644 --- a/src/rdds/gicam/vcf_inference/infer_vcf.py +++ b/src/rdds/gicam/vcf_inference/infer_vcf.py @@ -26,8 +26,8 @@ def _infer_gicam_fn(vcf_file_path: str, vcf_reader = VCFReader(vcf_file_path) if not replace_overwrite_vrs_annotation: - vcf_reader.add_info_to_header({'ID': 'GICAM', - 'Description': 'Rank score from GICAM model (joint MIVMIR and Genmod) (5 points precision)', + vcf_reader.add_info_to_header({'ID': 'GicamScore', + 'Description': 'Rank score from GICAM model (joint MIVMIR and Genmod genetic models) (5 points precision)', 'Type': 'Float', 'Number': '1'}) # TODO: Add GICAM version to header @@ -49,7 +49,7 @@ def _infer_gicam_fn(vcf_file_path: str, if replace_overwrite_vrs_annotation: variant.INFO['MivmirScore'] = f'{score:.5f}' else: - variant.INFO['GICAM'] = f'{score:.5f}' + variant.INFO['GicamScore'] = f'{score:.5f}' vcf_writer.write_record(variant) vcf_writer.close() vcf_reader.close() diff --git a/src/tests/gicam/test_inference.py b/src/tests/gicam/test_inference.py index 39e727b0..30c1520f 100644 --- a/src/tests/gicam/test_inference.py +++ b/src/tests/gicam/test_inference.py @@ -19,7 +19,7 @@ def test_vcf_inference(work_dir, overwrite_vrs_annotation): infer_vcf(vcf_file_path=test_data_path, cpu_cores=1, replace_overwrite_vrs_annotation=overwrite_vrs_annotation) reader = VCFReader(output_file, 'r') - target_annotation = 'GICAM' + target_annotation = 'GicamScore' if overwrite_vrs_annotation: target_annotation = 'MivmirScore' assert target_annotation in reader.info_fields @@ -42,10 +42,10 @@ def test_vcf_inference_cli(work_dir, cpu_cores): shell=True, stderr=sp.STDOUT) reader = VCFReader(output_file, 'r') - assert 'GICAM' in reader.info_fields + assert 'GicamScore' in reader.info_fields for variant in list(reader): - assert isinstance(variant.INFO['GICAM'], float) - assert 0 <= variant.INFO['GICAM'] <= 1 + assert isinstance(variant.INFO['GicamScore'], float) + assert 0 <= variant.INFO['GicamScore'] <= 1 reader.close() def test_score_variant():