Variant annotations

Available GET parameters:

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allele-frequency-threshold = float 
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GET /lookup/7-151945072--T?add-all-data=1&format=api
HTTP 200 OK
Allow: GET, HEAD, OPTIONS
Cache-Control: max-age=0
Content-Type: application/json
ETag: "573cff5dd622eee29206e69ea5ee20b5"
Vary: Accept

{
    "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.2447dupA",
                    "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
                }
            ],
            "version": "08-Apr-2019"
        }
    ],
    "ensembl_transcripts": [
        {
            "items": [
                {
                    "name": "ENST00000262189.6",
                    "strand": "-",
                    "coding_impact": "nonsense",
                    "function": [
                        "NMD",
                        "coding"
                    ],
                    "hgvs": "c.2447dupA",
                    "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"
                },
                {
                    "name": "ENST00000355193.2",
                    "strand": "-",
                    "coding_impact": "nonsense",
                    "function": [
                        "NMD",
                        "coding"
                    ],
                    "hgvs": "c.2447dupA",
                    "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": "1"
                },
                {
                    "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": "1"
                }
            ],
            "version": "95"
        }
    ],
    "gnomad_exomes": [
        {
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            "version": "2.0.2",
            "as_filterstatus": "PASS",
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            "an": 164498,
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            "ac_asj": 3199,
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            "hom": 0,
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            "hom_afr": 0,
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            "af_afr": 0.47217490062464507,
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            "af_male": 0.48782585682149,
            "af_female": 0.48699433711761997,
            "indel_original_representation": "151945071:1:GT",
            "main_data": "ƒ = 0.487"
        }
    ],
    "gnomad_exomes_coverage": [
        {
            "version": "2.0.2",
            "coverage_mean": [
                99.3499984741211
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            "coverage_median": [
                100.0
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            "coverage_20_frequency": [
                0.99969481490524
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    "gnomad_genomes": [
        {
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            "hom_afr": 0,
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            "indel_original_representation": "151945071:1:GT",
            "main_data": "ƒ = 0.483"
        }
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    "gnomad_genomes_coverage": [
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            "version": "2.0.2",
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                92.19999694824219
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            "coverage_20_frequency": [
                1.0
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    ],
    "gerp": [
        {
            "version": "2010",
            "gerp_nr": [
                5.670000076293945
            ],
            "gerp_rs": [
                5.670000076293945
            ]
        }
    ],
    "isb_kaviar3": [
        {
            "version": "4-Feb-2016",
            "ac": [
                891,
                4
            ],
            "an": [
                155504,
                155504
            ],
            "main_data": "ƒ = 0.00573,ƒ = 2.57e-05"
        }
    ],
    "ncbi_dbsnp": [
        {
            "version": "build 151",
            "rsid": [
                150073007
            ]
        }
    ],
    "sanger_cosmic_public": [
        {
            "version": "v86",
            "items": [
                {
                    "id": "COSM289942",
                    "num_samples": 8,
                    "is_consistent": true
                },
                {
                    "id": "COSM289943",
                    "num_samples": 8,
                    "is_consistent": true
                },
                {
                    "id": "COSM5446319",
                    "num_samples": 13,
                    "is_consistent": true
                },
                {
                    "id": "COSM5446318",
                    "num_samples": 13,
                    "is_consistent": true
                }
            ]
        }
    ],
    "ncbi_clinvar2": [
        {
            "version": "05-Apr-2019",
            "review_status": "criteria provided, single submitter",
            "review_stars": 1,
            "variation_id": 403020,
            "num_submitters": 1,
            "pub_med_references": null,
            "clinical_significance": [
                "Benign"
            ],
            "last_evaluation": "20160425",
            "origin": [
                "germline"
            ],
            "accessions": [
                {
                    "review_description": "Benign",
                    "review_status": "criteria provided, single submitter",
                    "variation_id": 403020,
                    "diseases": [
                        {
                            "symbols": {
                                "medgen": "CN169374"
                            },
                            "names": [
                                "Allhighlypenetrant"
                            ]
                        }
                    ],
                    "submission_description": [
                        ""
                    ],
                    "variant_id": 10190071519450720005,
                    "title": "NM_170606.2(KMT2C):c.2447dupA (p.Tyr816Terfs) AND not specified",
                    "clinical_significance": [
                        "Benign"
                    ],
                    "allele_id": 390552,
                    "accession_id": "RCV000455198",
                    "date_created": 20170408,
                    "submissions": [
                        {
                            "method": "clinical testing",
                            "review_description": "Benign",
                            "submitter_date": 20170403,
                            "date_updated": 20190331,
                            "accession_id": "SCV000539482",
                            "origin": "germline",
                            "submitter_name": "Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine",
                            "clinical_significance": [
                                "Benign"
                            ],
                            "review_date": 20160425,
                            "review_status": "criteria provided, single submitter",
                            "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"
                            ]
                        }
                    ],
                    "review_date": 20160425,
                    "review_stars": 1
                }
            ],
            "main_data": "benign **1**"
        }
    ],
    "pub_med_articles": {
        "24033266": {
            "journal": "Clinical genetics",
            "authors": [
                "Duzkale, H",
                "Shen, J",
                "McLaughlin, H",
                "Alfares, A",
                "Kelly, MA",
                "Pugh, TJ",
                "Funke, BH",
                "Rehm, HL",
                "Lebo, MS"
            ],
            "title": "A systematic approach to assessing the clinical significance of genetic variants.",
            "date_completed": 20140603,
            "format": "Article",
            "abstract": "Molecular genetic testing informs diagnosis, prognosis, and risk assessment for patients and their family members. Recent advances in low-cost, high-throughput DNA sequencing and computing technologies have enabled the rapid expansion of genetic test content, resulting in dramatically increased numbers of DNA variants identified per test. To address this challenge, our laboratory has developed a systematic approach to thorough and efficient assessments of variants for pathogenicity determination. We first search for existing data in publications and databases including internal, collaborative and public resources. We then perform full evidence-based assessments through statistical analyses of observations in the general population and disease cohorts, evaluation of experimental data from in vivo or in vitro studies, and computational predictions of potential impacts of each variant. Finally, we weigh all evidence to reach an overall conclusion on the potential for each variant to be disease causing. In this report, we highlight the principles of variant assessment, address the caveats and pitfalls, and provide examples to illustrate the process. By sharing our experience and providing a framework for variant assessment, including access to a freely available customizable tool, we hope to help move towards standardized and consistent approaches to variant assessment.",
            "date_published": 20131100,
            "journal_issue": "volume:84, issue:5",
            "journal_abbreviation": "Clin. Genet.",
            "pub_med_id": 24033266
        }
    }
}