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GeneBe API Showcase

This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.

API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.

Documentation & Advanced Usage

Complete API documentation:docs.genebe.net/docs/api/overview/

Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/

Python client for pandas:pypi.org/project/genebe/

Java CLI for VCF files:github.com/pstawinski/genebe-cli

All tools documented at:docs.genebe.net

API Request Examples for Variant: 1-237726282-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=237726282&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 237726282,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000366574.7",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 75,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10699C>T",
          "hgvs_p": "p.Arg3567Cys",
          "transcript": "NM_001035.3",
          "protein_id": "NP_001026.2",
          "transcript_support_level": null,
          "aa_start": 3567,
          "aa_end": null,
          "aa_length": 4967,
          "cds_start": 10699,
          "cds_end": null,
          "cds_length": 14904,
          "cdna_start": 11037,
          "cdna_end": null,
          "cdna_length": 16583,
          "mane_select": "ENST00000366574.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 75,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10699C>T",
          "hgvs_p": "p.Arg3567Cys",
          "transcript": "ENST00000366574.7",
          "protein_id": "ENSP00000355533.2",
          "transcript_support_level": 1,
          "aa_start": 3567,
          "aa_end": null,
          "aa_length": 4967,
          "cds_start": 10699,
          "cds_end": null,
          "cds_length": 14904,
          "cdna_start": 11037,
          "cdna_end": null,
          "cdna_length": 16583,
          "mane_select": "NM_001035.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 75,
          "exon_rank_end": null,
          "exon_count": 106,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10699C>T",
          "hgvs_p": "p.Arg3567Cys",
          "transcript": "ENST00000661330.2",
          "protein_id": "ENSP00000499393.2",
          "transcript_support_level": null,
          "aa_start": 3567,
          "aa_end": null,
          "aa_length": 4973,
          "cds_start": 10699,
          "cds_end": null,
          "cds_length": 14922,
          "cdna_start": 11037,
          "cdna_end": null,
          "cdna_length": 16601,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 73,
          "exon_rank_end": null,
          "exon_count": 104,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "n.*1734C>T",
          "hgvs_p": null,
          "transcript": "ENST00000609119.2",
          "protein_id": "ENSP00000499659.2",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 16525,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 73,
          "exon_rank_end": null,
          "exon_count": 104,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "n.*1734C>T",
          "hgvs_p": null,
          "transcript": "ENST00000609119.2",
          "protein_id": "ENSP00000499659.2",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 16525,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 75,
          "exon_rank_end": null,
          "exon_count": 106,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10699C>T",
          "hgvs_p": "p.Arg3567Cys",
          "transcript": "ENST00000714021.1",
          "protein_id": "ENSP00000519311.1",
          "transcript_support_level": null,
          "aa_start": 3567,
          "aa_end": null,
          "aa_length": 4973,
          "cds_start": 10699,
          "cds_end": null,
          "cds_length": 14922,
          "cdna_start": 11037,
          "cdna_end": null,
          "cdna_length": 16601,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 73,
          "exon_rank_end": null,
          "exon_count": 103,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10663C>T",
          "hgvs_p": "p.Arg3555Cys",
          "transcript": "ENST00000714019.1",
          "protein_id": "ENSP00000519309.1",
          "transcript_support_level": null,
          "aa_start": 3555,
          "aa_end": null,
          "aa_length": 4955,
          "cds_start": 10663,
          "cds_end": null,
          "cds_length": 14868,
          "cdna_start": 11001,
          "cdna_end": null,
          "cdna_length": 16547,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 72,
          "exon_rank_end": null,
          "exon_count": 102,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10588C>T",
          "hgvs_p": "p.Arg3530Cys",
          "transcript": "ENST00000714018.1",
          "protein_id": "ENSP00000519308.1",
          "transcript_support_level": null,
          "aa_start": 3530,
          "aa_end": null,
          "aa_length": 4930,
          "cds_start": 10588,
          "cds_end": null,
          "cds_length": 14793,
          "cdna_start": 10926,
          "cdna_end": null,
          "cdna_length": 16472,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 59,
          "exon_rank_end": null,
          "exon_count": 89,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.8734C>T",
          "hgvs_p": "p.Arg2912Cys",
          "transcript": "ENST00000714022.1",
          "protein_id": "ENSP00000519312.1",
          "transcript_support_level": null,
          "aa_start": 2912,
          "aa_end": null,
          "aa_length": 4312,
          "cds_start": 8734,
          "cds_end": null,
          "cds_length": 12939,
          "cdna_start": 9166,
          "cdna_end": null,
          "cdna_length": 14712,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 76,
          "exon_rank_end": null,
          "exon_count": 107,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10729C>T",
          "hgvs_p": "p.Arg3577Cys",
          "transcript": "XM_006711802.4",
          "protein_id": "XP_006711865.1",
          "transcript_support_level": null,
          "aa_start": 3577,
          "aa_end": null,
          "aa_length": 4985,
          "cds_start": 10729,
          "cds_end": null,
          "cds_length": 14958,
          "cdna_start": 11067,
          "cdna_end": null,
          "cdna_length": 16637,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 76,
          "exon_rank_end": null,
          "exon_count": 107,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10726C>T",
          "hgvs_p": "p.Arg3576Cys",
          "transcript": "XM_006711803.4",
          "protein_id": "XP_006711866.1",
          "transcript_support_level": null,
          "aa_start": 3576,
          "aa_end": null,
          "aa_length": 4984,
          "cds_start": 10726,
          "cds_end": null,
          "cds_length": 14955,
          "cdna_start": 11064,
          "cdna_end": null,
          "cdna_length": 16634,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 75,
          "exon_rank_end": null,
          "exon_count": 106,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10708C>T",
          "hgvs_p": "p.Arg3570Cys",
          "transcript": "XM_017002028.2",
          "protein_id": "XP_016857517.1",
          "transcript_support_level": null,
          "aa_start": 3570,
          "aa_end": null,
          "aa_length": 4978,
          "cds_start": 10708,
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          "cdna_start": 11046,
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          "cdna_length": 16616,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 76,
          "exon_rank_end": null,
          "exon_count": 106,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10729C>T",
          "hgvs_p": "p.Arg3577Cys",
          "transcript": "XM_006711804.4",
          "protein_id": "XP_006711867.1",
          "transcript_support_level": null,
          "aa_start": 3577,
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          "aa_length": 4977,
          "cds_start": 10729,
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          "cdna_start": 11067,
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          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 75,
          "exon_rank_end": null,
          "exon_count": 106,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10699C>T",
          "hgvs_p": "p.Arg3567Cys",
          "transcript": "XM_006711805.4",
          "protein_id": "XP_006711868.1",
          "transcript_support_level": null,
          "aa_start": 3567,
          "aa_end": null,
          "aa_length": 4975,
          "cds_start": 10699,
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          "cds_length": 14928,
          "cdna_start": 11037,
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          "cdna_length": 16607,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
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          "canonical": false,
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          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 75,
          "exon_rank_end": null,
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          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10696C>T",
          "hgvs_p": "p.Arg3566Cys",
          "transcript": "XM_047427317.1",
          "protein_id": "XP_047283273.1",
          "transcript_support_level": null,
          "aa_start": 3566,
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          "cds_start": 10696,
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          "cdna_start": 11034,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 73,
          "exon_rank_end": null,
          "exon_count": 104,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10492C>T",
          "hgvs_p": "p.Arg3498Cys",
          "transcript": "XM_006711808.4",
          "protein_id": "XP_006711871.1",
          "transcript_support_level": null,
          "aa_start": 3498,
          "aa_end": null,
          "aa_length": 4906,
          "cds_start": 10492,
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          "cdna_start": 10830,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 72,
          "exon_rank_end": null,
          "exon_count": 103,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10462C>T",
          "hgvs_p": "p.Arg3488Cys",
          "transcript": "XM_047427329.1",
          "protein_id": "XP_047283285.1",
          "transcript_support_level": null,
          "aa_start": 3488,
          "aa_end": null,
          "aa_length": 4896,
          "cds_start": 10462,
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          "cds_length": 14691,
          "cdna_start": 10800,
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          "mane_select": null,
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          "feature": null
        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 106,
          "intron_rank": 74,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10690-805C>T",
          "hgvs_p": null,
          "transcript": "ENST00000660292.2",
          "protein_id": "ENSP00000499787.2",
          "transcript_support_level": null,
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          "mane_select": null,
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 105,
          "intron_rank": 74,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10690-805C>T",
          "hgvs_p": null,
          "transcript": "ENST00000659194.3",
          "protein_id": "ENSP00000499653.3",
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          "cds_start": -4,
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          "cdna_start": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 106,
          "intron_rank": 75,
          "intron_rank_end": null,
          "gene_symbol": "RYR2",
          "gene_hgnc_id": 10484,
          "hgvs_c": "c.10720-805C>T",
          "hgvs_p": null,
          "transcript": "XM_006711806.4",
          "protein_id": "XP_006711869.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 4973,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 14922,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 16601,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": 75,
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          "protein_id": "XP_047283297.1",
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        }
      ],
      "gene_symbol": "RYR2",
      "gene_hgnc_id": 10484,
      "dbsnp": "rs559154874",
      "frequency_reference_population": 0.00003343431,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 53,
      "gnomad_exomes_af": 0.0000327974,
      "gnomad_genomes_af": 0.0000394332,
      "gnomad_exomes_ac": 47,
      "gnomad_genomes_ac": 6,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.04163643717765808,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.019999999552965164,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.322,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.142,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.31,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.058,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.02,
      "spliceai_max_prediction": "Benign",
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": -12,
      "acmg_classification": "Benign",
      "acmg_criteria": "PP2,BP4_Strong,BP6,BS1,BS2",
      "acmg_by_gene": [
        {
          "score": -12,
          "benign_score": 13,
          "pathogenic_score": 1,
          "criteria": [
            "PP2",
            "BP4_Strong",
            "BP6",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000366574.7",
          "gene_symbol": "RYR2",
          "hgnc_id": 10484,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.10699C>T",
          "hgvs_p": "p.Arg3567Cys"
        }
      ],
      "clinvar_disease": "Cardiomyopathy,Cardiovascular phenotype,Catecholaminergic polymorphic ventricular tachycardia 1,RYR2-related disorder,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:3 LB:3",
      "phenotype_combined": "not provided|Cardiomyopathy|Cardiovascular phenotype|Catecholaminergic polymorphic ventricular tachycardia 1|RYR2-related disorder",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}