Variant Annotation
Available parameters and response documentation is available here
GET /lookup/7-151945072--T?add-all-data=1&format=api
{ "chromosome": "chr7", "alt": "T", "ref": "", "pos": 151945072, "variant_id": "10190071519450720005", "variant_type": "Insertion", "cytobands": "7q36.1", "refseq_transcripts": [ { "items": [ { "name": "NM_170606.3", "strand": "-", "coding_impact": "nonsense", "function": [ "NMD", "coding" ], "hgvs": "c.2447dup", "hgvs_p1": "Y816*", "hgvs_p3": "p.(Tyr816Ter)", "location": "exon 14 of 59 before position 635 of 719", "coding_location": "816 of 4912", "canonical": true, "gene_symbol": "KMT2C", "splice_distance": "-86", "ensembl_support_level": null, "ensembl_appris": null, "mane_select": "ENST00000262189.11", "mane_plus": null, "uniprot_id": null } ], "version": "221" } ], "ensembl_transcripts": [ { "items": [ { "name": "ENST00000262189.6", "strand": "-", "coding_impact": "nonsense", "function": [ "NMD", "coding" ], "hgvs": "c.2447dup", "hgvs_p1": "Y816*", "hgvs_p3": "p.(Tyr816Ter)", "location": "exon 14 of 59 before position 635 of 719", "coding_location": "816 of 4912", "canonical": true, "gene_symbol": "KMT2C", "splice_distance": "-86", "ensembl_support_level": "1", "ensembl_appris": "principal2", "mane_select": "NM_170606.3", "mane_plus": null, "uniprot_id": "Q8NEZ4" }, { "name": "ENST00000355193.2", "strand": "-", "coding_impact": "nonsense", "function": [ "NMD", "coding" ], "hgvs": "c.2447dup", "hgvs_p1": "Y816*", "hgvs_p3": "p.(Tyr816Ter)", "location": "exon 14 of 60 before position 635 of 719", "coding_location": "816 of 4969", "canonical": false, "gene_symbol": "KMT2C", "splice_distance": "-86", "ensembl_support_level": null, "ensembl_appris": null, "mane_select": null, "mane_plus": null, "uniprot_id": "Q8NEZ4" }, { "name": "ENST00000418673.1", "strand": "-", "coding_impact": "nonsense", "function": [ "NMD", "coding" ], "hgvs": "c.32dup", "hgvs_p1": "Y11*", "hgvs_p3": "p.(Tyr11Ter)", "location": "exon 1 of 6 before position 34 of 118", "coding_location": "11 of 227", "canonical": false, "gene_symbol": "KMT2C", "splice_distance": "-86", "ensembl_support_level": "5", "ensembl_appris": null, "mane_select": null, "mane_plus": null, "uniprot_id": null }, { "name": "ENST00000558084.1", "strand": "-", "coding_impact": null, "function": [ "non-coding exon" ], "hgvs": null, "hgvs_p1": null, "hgvs_p3": null, "location": "exon 14 of 59 before position 635 of 719", "coding_location": null, "canonical": false, "gene_symbol": "KMT2C", "splice_distance": "-86", "ensembl_support_level": null, "ensembl_appris": null, "mane_select": null, "mane_plus": null, "uniprot_id": null } ], "version": "110" } ], "gnomad_exomes": [ { "version": "2.1.1", "filter": "InbreedingCoeff;RF", "ac": 81747, "an": 167790, "af": 0.48719828356874667, "ac_afr": 3538, "ac_amr": 11304, "ac_asj": 3268, "ac_eas": 6142, "ac_eas_kor": 1169, "ac_eas_jpn": 59, "ac_eas_oea": 4914, "ac_fin": 7706, "ac_nfe": 38135, "ac_nfe_bgr": 993, "ac_nfe_est": 93, "ac_nfe_nwe": 13432, "ac_nfe_onf": 10619, "ac_nfe_seu": 3882, "ac_nfe_swe": 9116, "ac_oth": 1883, "ac_sas": 9771, "ac_afr_male": 1341, "ac_amr_male": 4636, "ac_asj_male": 1671, "ac_eas_male": 3014, "ac_fin_male": 4014, "ac_nfe_male": 21421, "ac_oth_male": 970, "ac_sas_male": 7438, "ac_afr_female": 2197, "ac_amr_female": 6668, "ac_asj_female": 1597, "ac_eas_female": 3128, "ac_fin_female": 3692, "ac_nfe_female": 16714, "ac_oth_female": 913, "ac_sas_female": 2333, "ac_male": 44505, "ac_female": 37242, "an_afr": 7504, "an_amr": 23102, "an_asj": 6766, "an_eas": 12322, "an_eas_kor": 2350, "an_eas_jpn": 118, "an_eas_oea": 9854, "an_fin": 15734, "an_nfe": 78650, "an_nfe_bgr": 2018, "an_nfe_est": 192, "an_nfe_nwe": 28022, "an_nfe_onf": 21774, "an_nfe_seu": 8030, "an_nfe_swe": 18614, "an_oth": 3936, "an_sas": 19776, "an_afr_male": 2848, "an_amr_male": 9490, "an_asj_male": 3466, "an_eas_male": 6050, "an_fin_male": 8194, "an_nfe_male": 44160, "an_oth_male": 2022, "an_sas_male": 15044, "an_afr_female": 4656, "an_amr_female": 13612, "an_asj_female": 3300, "an_eas_female": 6272, "an_fin_female": 7540, "an_nfe_female": 34490, "an_oth_female": 1914, "an_sas_female": 4732, "an_male": 91274, "an_female": 76516, "age_hist_het_under_30": 1591, "age_hist_het_30_35": 2238, "age_hist_het_35_40": 2966, "age_hist_het_40_45": 5541, "age_hist_het_45_50": 6766, "age_hist_het_50_55": 8176, "age_hist_het_55_60": 7573, "age_hist_het_60_65": 6858, "age_hist_het_65_70": 5847, "age_hist_het_70_75": 3942, "age_hist_het_75_80": 2726, "age_hist_het_over_80": 1319, "variant_type": "mixed", "segdup": true, "original_variant": "7-151945071-G-GT", "main_data": "ƒ = 0.487" } ], "gnomad_exomes_coverage": [ { "version": "2.1", "coverage_mean": [ 99.37200164794922 ], "coverage_median": [ 100.0 ], "coverage_20_frequency": [ 1.0 ] } ], "gnomad_genomes": [ { "version": "2.1.1", "filter": "InbreedingCoeff", "ac": 10703, "an": 22162, "af": 0.4829437776373973, "ac_afr": 2353, "ac_amr": 311, "ac_asj": 98, "ac_eas": 633, "ac_fin": 1243, "ac_nfe": 5677, "ac_nfe_est": 1714, "ac_nfe_nwe": 3153, "ac_nfe_onf": 781, "ac_nfe_seu": 29, "ac_oth": 388, "ac_afr_male": 1372, "ac_amr_male": 152, "ac_asj_male": 70, "ac_eas_male": 424, "ac_fin_male": 591, "ac_nfe_male": 3171, "ac_oth_male": 176, "ac_afr_female": 981, "ac_amr_female": 159, "ac_asj_female": 28, "ac_eas_female": 209, "ac_fin_female": 652, "ac_nfe_female": 2506, "ac_oth_female": 212, "ac_male": 5956, "ac_female": 4747, "an_afr": 4982, "an_amr": 634, "an_asj": 198, "an_eas": 1272, "an_fin": 2564, "an_nfe": 11714, "an_nfe_est": 3496, "an_nfe_nwe": 6530, "an_nfe_onf": 1628, "an_nfe_seu": 60, "an_oth": 798, "an_afr_male": 2914, "an_amr_male": 308, "an_asj_male": 142, "an_eas_male": 852, "an_fin_male": 1216, "an_nfe_male": 6566, "an_oth_male": 368, "an_afr_female": 2068, "an_amr_female": 326, "an_asj_female": 56, "an_eas_female": 420, "an_fin_female": 1348, "an_nfe_female": 5148, "an_oth_female": 430, "an_male": 12366, "an_female": 9796, "age_hist_het_under_30": 1536, "age_hist_het_30_35": 433, "age_hist_het_35_40": 480, "age_hist_het_40_45": 673, "age_hist_het_45_50": 955, "age_hist_het_50_55": 1200, "age_hist_het_55_60": 931, "age_hist_het_60_65": 736, "age_hist_het_65_70": 495, "age_hist_het_70_75": 280, "age_hist_het_75_80": 123, "age_hist_het_over_80": 51, "variant_type": "mixed", "segdup": true, "original_variant": "7-151945071-G-GT", "main_data": "ƒ = 0.483" } ], "gnomad_genomes_coverage": [ { "version": "2.1", "coverage_mean": [ 92.58300018310547 ], "coverage_median": [ 100.0 ], "coverage_20_frequency": [ 1.0 ] } ], "gerp": [ { "version": "2010", "gerp_nr": [ 5.670000076293945, 5.670000076293945, 5.670000076293945 ], "gerp_rs": [ 2.509999990463257, 5.670000076293945, 5.670000076293945 ] } ], "isb_kaviar3": [ { "version": "4-Feb-2016", "ac": [ 891, 4 ], "an": [ 155504, 155504 ], "main_data": null } ], "ncbi_dbsnp": [ { "version": "build 156", "rsid": [ 150073007 ] } ], "ncbi_clinvar2": [ { "version": "01-Mar-2024", "review_status": "criteria provided, single submitter", "review_stars": 1, "variation_id": 403020, "num_submitters": 2, "pub_med_references": null, "clinical_significance": [ "Benign" ], "last_evaluation": "20230930", "origin": null, "accessions": [ { "variation_id": 403020, "accession_id": "RCV001251811", "allele_id": 390552, "clinical_significance": [ "Likely benign" ], "submissions": [ { "submitter_name": "Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille", "submission_description": [], "submitter_date": 20200505, "review_description": "Likely benign", "review_status": "no assertion criteria provided", "review_date": 20190101, "origin": "uniparental", "method": "clinical testing", "finding": [ { "symbols": { "hp": "HP:0001249" }, "normalized_phenotype": [ "Intellectual Disability" ] } ], "date_updated": 20200815, "clinical_significance": [ "Likely benign" ], "accession_id": "SCV001427553" } ], "date_created": 20200815, "finding": [ { "pub_med_references": [ 21956720, 25157020, 34131312, 34211152 ], "normalized_phenotype": [ "Intellectual Disability" ], "symbols": { "medgen": "C3714756", "mesh": "D008607", "mondo": "MONDO:0001071", "human_phenotype_ontology": "HP:0007180" }, "names": [ "Intellectual Disability", "Intellectual Functioning Disability", "Intellectual Disability", "Intellectual Developmental Disorder" ] } ], "review_date": 20190101, "review_status": "no assertion criteria provided", "review_description": "Likely benign", "title": "NM_170606.3(KMT2C):c.2447dup (p.Tyr816Ter) AND Intellectual disability", "review_stars": 0, "submission_description": [], "variant_id": 10190071519450720005 }, { "variation_id": 403020, "accession_id": "RCV000455198", "diseases": [ { "symbols": { "medgen": "CN169374" }, "names": [ "Not Specified", "Allhighlypenetrant" ] } ], "allele_id": 390552, "clinical_significance": [ "Benign" ], "submissions": [ { "submitter_name": "Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine", "submission_description": [ "Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: frequency" ], "submitter_date": 20170403, "review_description": "Benign", "review_status": "criteria provided, single submitter", "review_date": 20160425, "origin": "germline", "method": "clinical testing", "date_updated": 20170410, "clinical_significance": [ "Benign" ], "diseases": [ { "names": [ "Not Specified" ] } ], "accession_id": "SCV000539482" } ], "date_created": 20170410, "review_date": 20160425, "review_status": "criteria provided, single submitter", "review_description": "Benign", "title": "NM_170606.3(KMT2C):c.2447dup (p.Tyr816Ter) AND not specified", "review_stars": 1, "submission_description": [], "variant_id": 10190071519450720005 } ], "main_data": "benign **1**", "names": [ "NM_170606.3(KMT2C):c.2447dup (p.Tyr816Ter)", "p.Tyr816X" ], "variant_type": "Duplication" } ], "publications": { "publications": [ { "referenced_by": [ "ClinVar" ], "pub_med_id": 34211152 }, { "referenced_by": [ "ClinVar" ], "pub_med_id": 34131312 }, { "referenced_by": [ "VarSome AI", "VarSome AI Variant" ], "pub_med_id": 32429658 }, { "referenced_by": [ "ClinVar" ], "pub_med_id": 25157020 }, { "referenced_by": [ "ClinVar" ], "pub_med_id": 21956720 } ], "genes": [ { "publications": [ { "referenced_by": [ "VarSome AI" ], "pub_med_id": 38311546 }, { "referenced_by": [ "VarSome AI" ], "pub_med_id": 38146907 }, { "referenced_by": [ "VarSome AI" ], "pub_med_id": 37937729 }, { "referenced_by": [ "VarSome AI" ], "pub_med_id": 37284406 }, { "referenced_by": [ "VarSome AI" ], "pub_med_id": 37231433 }, { "referenced_by": [ "VarSome AI" ], "pub_med_id": 36672956 }, { "referenced_by": [ "GenCC" ], "pub_med_id": 36360262 }, { "referenced_by": [ "VarSome AI" ], "pub_med_id": 36333792 }, { "referenced_by": [ "VarSome AI" ], "pub_med_id": 35893033 }, { "referenced_by": [ "VarSome AI" ], "pub_med_id": 35739266 }, { "referenced_by": [ "GenCC", "VarSome AI" ], "pub_med_id": 35685914 }, { "referenced_by": [ "VarSome AI" ], "pub_med_id": 35685441 }, { 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