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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: 4-54736745-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=54736745&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "4",
      "pos": 54736745,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000288135.6",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2621C>T",
          "hgvs_p": "p.Pro874Leu",
          "transcript": "NM_000222.3",
          "protein_id": "NP_000213.1",
          "transcript_support_level": null,
          "aa_start": 874,
          "aa_end": null,
          "aa_length": 976,
          "cds_start": 2621,
          "cds_end": null,
          "cds_length": 2931,
          "cdna_start": 2679,
          "cdna_end": null,
          "cdna_length": 5147,
          "mane_select": "ENST00000288135.6",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2621C>T",
          "hgvs_p": "p.Pro874Leu",
          "transcript": "ENST00000288135.6",
          "protein_id": "ENSP00000288135.6",
          "transcript_support_level": 1,
          "aa_start": 874,
          "aa_end": null,
          "aa_length": 976,
          "cds_start": 2621,
          "cds_end": null,
          "cds_length": 2931,
          "cdna_start": 2679,
          "cdna_end": null,
          "cdna_length": 5147,
          "mane_select": "NM_000222.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2609C>T",
          "hgvs_p": "p.Pro870Leu",
          "transcript": "ENST00000412167.7",
          "protein_id": "ENSP00000390987.3",
          "transcript_support_level": 1,
          "aa_start": 870,
          "aa_end": null,
          "aa_length": 972,
          "cds_start": 2609,
          "cds_end": null,
          "cds_length": 2919,
          "cdna_start": 2701,
          "cdna_end": null,
          "cdna_length": 5126,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2624C>T",
          "hgvs_p": "p.Pro875Leu",
          "transcript": "NM_001385284.1",
          "protein_id": "NP_001372213.1",
          "transcript_support_level": null,
          "aa_start": 875,
          "aa_end": null,
          "aa_length": 977,
          "cds_start": 2624,
          "cds_end": null,
          "cds_length": 2934,
          "cdna_start": 2682,
          "cdna_end": null,
          "cdna_length": 5150,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2624C>T",
          "hgvs_p": "p.Pro875Leu",
          "transcript": "ENST00000687109.1",
          "protein_id": "ENSP00000509371.1",
          "transcript_support_level": null,
          "aa_start": 875,
          "aa_end": null,
          "aa_length": 977,
          "cds_start": 2624,
          "cds_end": null,
          "cds_length": 2934,
          "cdna_start": 2726,
          "cdna_end": null,
          "cdna_length": 5249,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2621C>T",
          "hgvs_p": "p.Pro874Leu",
          "transcript": "NM_001385290.1",
          "protein_id": "NP_001372219.1",
          "transcript_support_level": null,
          "aa_start": 874,
          "aa_end": null,
          "aa_length": 976,
          "cds_start": 2621,
          "cds_end": null,
          "cds_length": 2931,
          "cdna_start": 2679,
          "cdna_end": null,
          "cdna_length": 5147,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2621C>T",
          "hgvs_p": "p.Pro874Leu",
          "transcript": "ENST00000689832.1",
          "protein_id": "ENSP00000509084.1",
          "transcript_support_level": null,
          "aa_start": 874,
          "aa_end": null,
          "aa_length": 976,
          "cds_start": 2621,
          "cds_end": null,
          "cds_length": 2931,
          "cdna_start": 2669,
          "cdna_end": null,
          "cdna_length": 5098,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2618C>T",
          "hgvs_p": "p.Pro873Leu",
          "transcript": "NM_001385285.1",
          "protein_id": "NP_001372214.1",
          "transcript_support_level": null,
          "aa_start": 873,
          "aa_end": null,
          "aa_length": 975,
          "cds_start": 2618,
          "cds_end": null,
          "cds_length": 2928,
          "cdna_start": 2676,
          "cdna_end": null,
          "cdna_length": 5144,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2618C>T",
          "hgvs_p": "p.Pro873Leu",
          "transcript": "ENST00000692783.1",
          "protein_id": "ENSP00000508733.1",
          "transcript_support_level": null,
          "aa_start": 873,
          "aa_end": null,
          "aa_length": 975,
          "cds_start": 2618,
          "cds_end": null,
          "cds_length": 2928,
          "cdna_start": 2710,
          "cdna_end": null,
          "cdna_length": 5230,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2612C>T",
          "hgvs_p": "p.Pro871Leu",
          "transcript": "NM_001385288.1",
          "protein_id": "NP_001372217.1",
          "transcript_support_level": null,
          "aa_start": 871,
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          "aa_length": 973,
          "cds_start": 2612,
          "cds_end": null,
          "cds_length": 2922,
          "cdna_start": 2670,
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          "cdna_length": 5138,
          "mane_select": null,
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        },
        {
          "aa_ref": "P",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
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          "intron_rank": null,
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          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2612C>T",
          "hgvs_p": "p.Pro871Leu",
          "transcript": "ENST00000690543.1",
          "protein_id": "ENSP00000508831.1",
          "transcript_support_level": null,
          "aa_start": 871,
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          "aa_length": 973,
          "cds_start": 2612,
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          "cdna_start": 2670,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
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          "exon_count": 21,
          "intron_rank": null,
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          "gene_symbol": "KIT",
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          "hgvs_c": "c.2609C>T",
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          "protein_id": "NP_001087241.1",
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          "cds_start": 2609,
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        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "KIT",
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          "hgvs_c": "c.2609C>T",
          "hgvs_p": "p.Pro870Leu",
          "transcript": "NM_001385292.1",
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        {
          "aa_ref": "P",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
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          "exon_count": 21,
          "intron_rank": null,
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          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2609C>T",
          "hgvs_p": "p.Pro870Leu",
          "transcript": "ENST00000687295.1",
          "protein_id": "ENSP00000509450.1",
          "transcript_support_level": null,
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        {
          "aa_ref": "P",
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          "gene_symbol": "KIT",
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          "feature": null
        },
        {
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          "protein_coding": true,
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          "consequences": [
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          ],
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          "intron_rank": null,
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          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2606C>T",
          "hgvs_p": "p.Pro869Leu",
          "transcript": "ENST00000686011.1",
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          "transcript_support_level": null,
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        {
          "aa_ref": "P",
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          "protein_coding": true,
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          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
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          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "c.2486C>T",
          "hgvs_p": "p.Pro829Leu",
          "transcript": "ENST00000687246.1",
          "protein_id": "ENSP00000509114.1",
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        },
        {
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          "consequences": [
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          ],
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          "intron_rank": null,
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          "gene_symbol": "KIT",
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          "hgvs_c": "c.2111C>T",
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        },
        {
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "n.1313C>T",
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        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "n.2699C>T",
          "hgvs_p": null,
          "transcript": "ENST00000685269.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "aa_length": null,
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          "cds_length": null,
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          "cdna_length": 5116,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
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          "intron_rank": null,
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          "gene_symbol": "KIT",
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        },
        {
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          "consequences": [
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          "exon_rank": 2,
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          "gene_symbol": "KIT",
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          "cdna_length": 1806,
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        },
        {
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          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
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          "exon_rank": 19,
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          "intron_rank": null,
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          "gene_symbol": "KIT",
          "gene_hgnc_id": 6342,
          "hgvs_c": "n.2718C>T",
          "hgvs_p": null,
          "transcript": "ENST00000692991.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
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          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 4977,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "KIT",
      "gene_hgnc_id": 6342,
      "dbsnp": "rs753419764",
      "frequency_reference_population": 0.00001548964,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 25,
      "gnomad_exomes_af": 0.0000157336,
      "gnomad_genomes_af": 0.0000131453,
      "gnomad_exomes_ac": 23,
      "gnomad_genomes_ac": 2,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.784849226474762,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.019999999552965164,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.463,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.3096,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.08,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 4.938,
      "phylop100way_prediction": "Uncertain_significance",
      "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": -2,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "PP2,PP3,BS2",
      "acmg_by_gene": [
        {
          "score": -2,
          "benign_score": 4,
          "pathogenic_score": 2,
          "criteria": [
            "PP2",
            "PP3",
            "BS2"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000288135.6",
          "gene_symbol": "KIT",
          "hgnc_id": 6342,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.2621C>T",
          "hgvs_p": "p.Pro874Leu"
        }
      ],
      "clinvar_disease": "Gastrointestinal stromal tumor,Hereditary cancer-predisposing syndrome,not provided",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "US:5",
      "phenotype_combined": "Gastrointestinal stromal tumor|Hereditary cancer-predisposing syndrome|not provided",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}