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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: 12-109786798-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=109786798&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "12",
      "pos": 109786798,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000261740.7",
      "consequences": [
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "c.2248G>A",
          "hgvs_p": "p.Val750Ile",
          "transcript": "NM_021625.5",
          "protein_id": "NP_067638.3",
          "transcript_support_level": null,
          "aa_start": 750,
          "aa_end": null,
          "aa_length": 871,
          "cds_start": 2248,
          "cds_end": null,
          "cds_length": 2616,
          "cdna_start": 2328,
          "cdna_end": null,
          "cdna_length": 3228,
          "mane_select": "ENST00000261740.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "c.2248G>A",
          "hgvs_p": "p.Val750Ile",
          "transcript": "ENST00000261740.7",
          "protein_id": "ENSP00000261740.2",
          "transcript_support_level": 1,
          "aa_start": 750,
          "aa_end": null,
          "aa_length": 871,
          "cds_start": 2248,
          "cds_end": null,
          "cds_length": 2616,
          "cdna_start": 2328,
          "cdna_end": null,
          "cdna_length": 3228,
          "mane_select": "NM_021625.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "c.2248G>A",
          "hgvs_p": "p.Val750Ile",
          "transcript": "ENST00000418703.7",
          "protein_id": "ENSP00000406191.2",
          "transcript_support_level": 1,
          "aa_start": 750,
          "aa_end": null,
          "aa_length": 871,
          "cds_start": 2248,
          "cds_end": null,
          "cds_length": 2616,
          "cdna_start": 2343,
          "cdna_end": null,
          "cdna_length": 3245,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "c.2146G>A",
          "hgvs_p": "p.Val716Ile",
          "transcript": "ENST00000536838.1",
          "protein_id": "ENSP00000444336.1",
          "transcript_support_level": 1,
          "aa_start": 716,
          "aa_end": null,
          "aa_length": 837,
          "cds_start": 2146,
          "cds_end": null,
          "cds_length": 2514,
          "cdna_start": 2146,
          "cdna_end": null,
          "cdna_length": 2514,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "c.2107G>A",
          "hgvs_p": "p.Val703Ile",
          "transcript": "ENST00000541794.5",
          "protein_id": "ENSP00000442167.1",
          "transcript_support_level": 1,
          "aa_start": 703,
          "aa_end": null,
          "aa_length": 824,
          "cds_start": 2107,
          "cds_end": null,
          "cds_length": 2475,
          "cdna_start": 2107,
          "cdna_end": null,
          "cdna_length": 2475,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "c.2068G>A",
          "hgvs_p": "p.Val690Ile",
          "transcript": "ENST00000537083.5",
          "protein_id": "ENSP00000442738.1",
          "transcript_support_level": 1,
          "aa_start": 690,
          "aa_end": null,
          "aa_length": 811,
          "cds_start": 2068,
          "cds_end": null,
          "cds_length": 2436,
          "cdna_start": 2068,
          "cdna_end": null,
          "cdna_length": 2436,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "c.1927G>A",
          "hgvs_p": "p.Val643Ile",
          "transcript": "ENST00000544971.5",
          "protein_id": "ENSP00000443611.1",
          "transcript_support_level": 1,
          "aa_start": 643,
          "aa_end": null,
          "aa_length": 764,
          "cds_start": 1927,
          "cds_end": null,
          "cds_length": 2295,
          "cdna_start": 1927,
          "cdna_end": null,
          "cdna_length": 2295,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "n.*631G>A",
          "hgvs_p": null,
          "transcript": "ENST00000538125.5",
          "protein_id": "ENSP00000437449.1",
          "transcript_support_level": 1,
          "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": 2804,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "n.*631G>A",
          "hgvs_p": null,
          "transcript": "ENST00000538125.5",
          "protein_id": "ENSP00000437449.1",
          "transcript_support_level": 1,
          "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": 2804,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "c.2248G>A",
          "hgvs_p": "p.Val750Ile",
          "transcript": "ENST00000675670.1",
          "protein_id": "ENSP00000502135.1",
          "transcript_support_level": null,
          "aa_start": 750,
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          "cds_start": 2248,
          "cds_end": null,
          "cds_length": 2616,
          "cdna_start": 2697,
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          "cdna_length": 3597,
          "mane_select": null,
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        {
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          "protein_coding": true,
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          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
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          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "c.2146G>A",
          "hgvs_p": "p.Val716Ile",
          "transcript": "NM_001177431.1",
          "protein_id": "NP_001170902.1",
          "transcript_support_level": null,
          "aa_start": 716,
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          "aa_length": 837,
          "cds_start": 2146,
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          "cdna_start": 2146,
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          "mane_select": null,
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          "biotype": null,
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        },
        {
          "aa_ref": "V",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 12,
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          "exon_count": 14,
          "intron_rank": null,
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          "gene_symbol": "TRPV4",
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          "hgvs_c": "c.2107G>A",
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        {
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          "hgvs_c": "c.2068G>A",
          "hgvs_p": "p.Val690Ile",
          "transcript": "NM_147204.2",
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          "gene_symbol": "TRPV4",
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          "hgvs_c": "c.1927G>A",
          "hgvs_p": "p.Val643Ile",
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        {
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        {
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          "intron_rank": null,
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          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "c.2260G>A",
          "hgvs_p": "p.Val754Ile",
          "transcript": "XM_011538631.3",
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        },
        {
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          ],
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          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "c.2080G>A",
          "hgvs_p": "p.Val694Ile",
          "transcript": "XM_011538633.3",
          "protein_id": "XP_011536935.2",
          "transcript_support_level": null,
          "aa_start": 694,
          "aa_end": null,
          "aa_length": 815,
          "cds_start": 2080,
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          "cds_length": 2448,
          "cdna_start": 3119,
          "cdna_end": null,
          "cdna_length": 4021,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
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          "hgvs_c": "c.2068G>A",
          "hgvs_p": "p.Val690Ile",
          "transcript": "XM_047429294.1",
          "protein_id": "XP_047285250.1",
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          "aa_length": 811,
          "cds_start": 2068,
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          "cds_length": 2436,
          "cdna_start": 2148,
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          "cdna_length": 3050,
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        },
        {
          "aa_ref": "V",
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          "protein_coding": true,
          "strand": false,
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            "missense_variant"
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          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
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          "gene_symbol": "TRPV4",
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          "hgvs_c": "c.1927G>A",
          "hgvs_p": "p.Val643Ile",
          "transcript": "XM_047429295.1",
          "protein_id": "XP_047285251.1",
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          "aa_start": 643,
          "aa_end": null,
          "aa_length": 764,
          "cds_start": 1927,
          "cds_end": null,
          "cds_length": 2295,
          "cdna_start": 2007,
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          "cdna_length": 2909,
          "mane_select": null,
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "n.*1335G>A",
          "hgvs_p": null,
          "transcript": "ENST00000674908.1",
          "protein_id": "ENSP00000502012.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 3266,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "n.*1335G>A",
          "hgvs_p": null,
          "transcript": "ENST00000674908.1",
          "protein_id": "ENSP00000502012.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3266,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": null,
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "n.*12G>A",
          "hgvs_p": null,
          "transcript": "ENST00000675533.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 2326,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": null,
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRPV4",
          "gene_hgnc_id": 18083,
          "hgvs_c": "c.*78G>A",
          "hgvs_p": null,
          "transcript": "XM_011538634.3",
          "protein_id": "XP_011536936.2",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": 793,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2382,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3488,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "TRPV4",
      "gene_hgnc_id": 18083,
      "dbsnp": "rs148171058",
      "frequency_reference_population": 0.0015093217,
      "hom_count_reference_population": 7,
      "allele_count_reference_population": 2436,
      "gnomad_exomes_af": 0.00153996,
      "gnomad_genomes_af": 0.00121515,
      "gnomad_exomes_ac": 2251,
      "gnomad_genomes_ac": 185,
      "gnomad_exomes_homalt": 7,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.017172783613204956,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.38,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.094,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.16,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 1.204,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0,
      "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": -20,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
      "acmg_by_gene": [
        {
          "score": -20,
          "benign_score": 20,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000261740.7",
          "gene_symbol": "TRPV4",
          "hgnc_id": 18083,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.2248G>A",
          "hgvs_p": "p.Val750Ile"
        }
      ],
      "clinvar_disease": " Kozlowski type, autosomal dominant 8, distal hereditary motor,Brachyrachia (short spine dysplasia),Charcot-Marie-Tooth disease,Charcot-Marie-Tooth disease axonal type 2C,Inborn genetic diseases,Metatropic dysplasia,Neuronopathy,Scapuloperoneal spinal muscular atrophy,Spondylometaphyseal dysplasia,TRPV4-related disorder,not provided,not specified",
      "clinvar_classification": "Benign/Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:6 B:8",
      "phenotype_combined": "Scapuloperoneal spinal muscular atrophy|Brachyrachia (short spine dysplasia)|Spondylometaphyseal dysplasia, Kozlowski type|not provided|not specified|Charcot-Marie-Tooth disease|Charcot-Marie-Tooth disease axonal type 2C|Neuronopathy, distal hereditary motor, autosomal dominant 8|Metatropic dysplasia|Inborn genetic diseases|TRPV4-related disorder",
      "pathogenicity_classification_combined": "Benign/Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}