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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: 12-118016853-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=118016853&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "12",
      "pos": 118016853,
      "ref": "A",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "NM_007370.7",
      "consequences": [
        {
          "aa_ref": "Q",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.26A>G",
          "hgvs_p": "p.Gln9Arg",
          "transcript": "NM_007370.7",
          "protein_id": "NP_031396.1",
          "transcript_support_level": null,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 340,
          "cds_start": 26,
          "cds_end": null,
          "cds_length": 1023,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000454402.7",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_007370.7"
        },
        {
          "aa_ref": "Q",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.26A>G",
          "hgvs_p": "p.Gln9Arg",
          "transcript": "ENST00000454402.7",
          "protein_id": "ENSP00000408295.2",
          "transcript_support_level": 1,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 340,
          "cds_start": 26,
          "cds_end": null,
          "cds_length": 1023,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_007370.7",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000454402.7"
        },
        {
          "aa_ref": "Q",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.26A>G",
          "hgvs_p": "p.Gln9Arg",
          "transcript": "ENST00000900837.1",
          "protein_id": "ENSP00000570896.1",
          "transcript_support_level": null,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 340,
          "cds_start": 26,
          "cds_end": null,
          "cds_length": 1023,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000900837.1"
        },
        {
          "aa_ref": "Q",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.26A>G",
          "hgvs_p": "p.Gln9Arg",
          "transcript": "ENST00000900836.1",
          "protein_id": "ENSP00000570895.1",
          "transcript_support_level": null,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 338,
          "cds_start": 26,
          "cds_end": null,
          "cds_length": 1017,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000900836.1"
        },
        {
          "aa_ref": "Q",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.26A>G",
          "hgvs_p": "p.Gln9Arg",
          "transcript": "ENST00000900838.1",
          "protein_id": "ENSP00000570897.1",
          "transcript_support_level": null,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 338,
          "cds_start": 26,
          "cds_end": null,
          "cds_length": 1017,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000900838.1"
        },
        {
          "aa_ref": "Q",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.26A>G",
          "hgvs_p": "p.Gln9Arg",
          "transcript": "NM_001206801.3",
          "protein_id": "NP_001193730.1",
          "transcript_support_level": null,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 337,
          "cds_start": 26,
          "cds_end": null,
          "cds_length": 1014,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001206801.3"
        },
        {
          "aa_ref": "Q",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.26A>G",
          "hgvs_p": "p.Gln9Arg",
          "transcript": "ENST00000900839.1",
          "protein_id": "ENSP00000570898.1",
          "transcript_support_level": null,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 337,
          "cds_start": 26,
          "cds_end": null,
          "cds_length": 1014,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000900839.1"
        },
        {
          "aa_ref": "Q",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.26A>G",
          "hgvs_p": "p.Gln9Arg",
          "transcript": "ENST00000900840.1",
          "protein_id": "ENSP00000570899.1",
          "transcript_support_level": null,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 335,
          "cds_start": 26,
          "cds_end": null,
          "cds_length": 1008,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000900840.1"
        },
        {
          "aa_ref": "Q",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.26A>G",
          "hgvs_p": "p.Gln9Arg",
          "transcript": "ENST00000913934.1",
          "protein_id": "ENSP00000583993.1",
          "transcript_support_level": null,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 314,
          "cds_start": 26,
          "cds_end": null,
          "cds_length": 945,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000913934.1"
        },
        {
          "aa_ref": "Q",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.26A>G",
          "hgvs_p": "p.Gln9Arg",
          "transcript": "ENST00000913933.1",
          "protein_id": "ENSP00000583992.1",
          "transcript_support_level": null,
          "aa_start": 9,
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          "cds_start": 26,
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          "cds_length": 927,
          "cdna_start": null,
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        },
        {
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          ],
          "exon_rank": 1,
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          "exon_count": 8,
          "intron_rank": null,
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          "gene_symbol": "RFC5",
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          "hgvs_c": "c.26A>G",
          "hgvs_p": "p.Gln9Arg",
          "transcript": "ENST00000900841.1",
          "protein_id": "ENSP00000570900.1",
          "transcript_support_level": null,
          "aa_start": 9,
          "aa_end": null,
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          "cds_start": 26,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 1,
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          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "RFC5",
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          "hgvs_c": "c.-97A>G",
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          "transcript": "NM_001130113.3",
          "protein_id": "NP_001123585.1",
          "transcript_support_level": null,
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          "cds_start": null,
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          "cdna_start": null,
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          "mane_select": null,
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        },
        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "RFC5",
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          "hgvs_c": "c.-402A>G",
          "hgvs_p": null,
          "transcript": "NM_181578.5",
          "protein_id": "NP_853556.2",
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          "biotype": "protein_coding",
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        {
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          ],
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          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "RFC5",
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          "hgvs_c": "c.-402A>G",
          "hgvs_p": null,
          "transcript": "ENST00000392542.6",
          "protein_id": "ENSP00000376325.2",
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          "biotype": "protein_coding",
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        {
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          ],
          "exon_rank": 1,
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          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.-356A>G",
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          "protein_id": "NP_001333744.1",
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        {
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          ],
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          "exon_count": 6,
          "intron_rank": null,
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          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.-64A>G",
          "hgvs_p": null,
          "transcript": "ENST00000484086.6",
          "protein_id": "ENSP00000445917.1",
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          "gene_symbol": "RFC5",
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        {
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          "gene_symbol": "RFC5",
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        {
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          "strand": true,
          "consequences": [
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          ],
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          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.-260A>G",
          "hgvs_p": null,
          "transcript": "ENST00000535092.1",
          "protein_id": "ENSP00000438252.1",
          "transcript_support_level": 4,
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          "aa_length": 62,
          "cds_start": null,
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        {
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          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "c.-190-2219A>G",
          "hgvs_p": null,
          "transcript": "ENST00000449641.6",
          "protein_id": "ENSP00000393636.2",
          "transcript_support_level": 4,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 98,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 297,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000449641.6"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "n.151A>G",
          "hgvs_p": null,
          "transcript": "NR_144504.2",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "NR_144504.2"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "n.151A>G",
          "hgvs_p": null,
          "transcript": "XR_007063111.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "XR_007063111.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RFC5",
          "gene_hgnc_id": 9973,
          "hgvs_c": "n.151A>G",
          "hgvs_p": null,
          "transcript": "XR_007063112.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "XR_007063112.1"
        }
      ],
      "gene_symbol": "RFC5",
      "gene_hgnc_id": 9973,
      "dbsnp": "rs368901773",
      "frequency_reference_population": 0.000011775818,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 19,
      "gnomad_exomes_af": 0.0000109491,
      "gnomad_genomes_af": 0.0000197153,
      "gnomad_exomes_ac": 16,
      "gnomad_genomes_ac": 3,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.0817992091178894,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.022,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0719,
      "alphamissense_prediction": "Benign",
      "bayesdelnoaf_score": -0.64,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.807,
      "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": 0,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,BP4_Moderate",
      "acmg_by_gene": [
        {
          "score": 0,
          "benign_score": 2,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_007370.7",
          "gene_symbol": "RFC5",
          "hgnc_id": 9973,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.26A>G",
          "hgvs_p": "p.Gln9Arg"
        }
      ],
      "clinvar_disease": "not specified",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "not specified",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}