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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: 7-4784209-C-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=4784209&ref=C&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "7",
      "pos": 4784209,
      "ref": "C",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_014855.3",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr",
          "transcript": "NM_014855.3",
          "protein_id": "NP_055670.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 807,
          "cds_start": 628,
          "cds_end": null,
          "cds_length": 2424,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000649063.2",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_014855.3"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr",
          "transcript": "ENST00000649063.2",
          "protein_id": "ENSP00000497815.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 807,
          "cds_start": 628,
          "cds_end": null,
          "cds_length": 2424,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_014855.3",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000649063.2"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr",
          "transcript": "ENST00000865634.1",
          "protein_id": "ENSP00000535693.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 832,
          "cds_start": 628,
          "cds_end": null,
          "cds_length": 2499,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000865634.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr",
          "transcript": "ENST00000865636.1",
          "protein_id": "ENSP00000535695.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 830,
          "cds_start": 628,
          "cds_end": null,
          "cds_length": 2493,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000865636.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr",
          "transcript": "ENST00000963395.1",
          "protein_id": "ENSP00000633454.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 821,
          "cds_start": 628,
          "cds_end": null,
          "cds_length": 2466,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000963395.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr",
          "transcript": "ENST00000963389.1",
          "protein_id": "ENSP00000633448.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 816,
          "cds_start": 628,
          "cds_end": null,
          "cds_length": 2451,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000963389.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.790C>A",
          "hgvs_p": "p.Pro264Thr",
          "transcript": "ENST00000963390.1",
          "protein_id": "ENSP00000633449.1",
          "transcript_support_level": null,
          "aa_start": 264,
          "aa_end": null,
          "aa_length": 814,
          "cds_start": 790,
          "cds_end": null,
          "cds_length": 2445,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000963390.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr",
          "transcript": "ENST00000963393.1",
          "protein_id": "ENSP00000633452.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 813,
          "cds_start": 628,
          "cds_end": null,
          "cds_length": 2442,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000963393.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr",
          "transcript": "ENST00000963396.1",
          "protein_id": "ENSP00000633455.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 806,
          "cds_start": 628,
          "cds_end": null,
          "cds_length": 2421,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000963396.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr",
          "transcript": "ENST00000913390.1",
          "protein_id": "ENSP00000583449.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 792,
          "cds_start": 628,
          "cds_end": null,
          "cds_length": 2379,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000913390.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr",
          "transcript": "ENST00000963391.1",
          "protein_id": "ENSP00000633450.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 791,
          "cds_start": 628,
          "cds_end": null,
          "cds_length": 2376,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000963391.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr",
          "transcript": "ENST00000865635.1",
          "protein_id": "ENSP00000535694.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 760,
          "cds_start": 628,
          "cds_end": null,
          "cds_length": 2283,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000865635.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.373C>A",
          "hgvs_p": "p.Pro125Thr",
          "transcript": "ENST00000963392.1",
          "protein_id": "ENSP00000633451.1",
          "transcript_support_level": null,
          "aa_start": 125,
          "aa_end": null,
          "aa_length": 722,
          "cds_start": 373,
          "cds_end": null,
          "cds_length": 2169,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000963392.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr",
          "transcript": "ENST00000865637.1",
          "protein_id": "ENSP00000535696.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 691,
          "cds_start": 628,
          "cds_end": null,
          "cds_length": 2076,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000865637.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
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          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.160C>A",
          "hgvs_p": "p.Pro54Thr",
          "transcript": "NM_001364858.1",
          "protein_id": "NP_001351787.1",
          "transcript_support_level": null,
          "aa_start": 54,
          "aa_end": null,
          "aa_length": 651,
          "cds_start": 160,
          "cds_end": null,
          "cds_length": 1956,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001364858.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.292C>A",
          "hgvs_p": "p.Pro98Thr",
          "transcript": "XM_047421098.1",
          "protein_id": "XP_047277054.1",
          "transcript_support_level": null,
          "aa_start": 98,
          "aa_end": null,
          "aa_length": 695,
          "cds_start": 292,
          "cds_end": null,
          "cds_length": 2088,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047421098.1"
        },
        {
          "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": 10,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "c.366+2455C>A",
          "hgvs_p": null,
          "transcript": "ENST00000963394.1",
          "protein_id": "ENSP00000633453.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 492,
          "cds_start": null,
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          "cds_length": 1479,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000963394.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "n.386C>A",
          "hgvs_p": null,
          "transcript": "ENST00000477680.6",
          "protein_id": null,
          "transcript_support_level": 2,
          "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": "retained_intron",
          "feature": "ENST00000477680.6"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "n.483C>A",
          "hgvs_p": null,
          "transcript": "ENST00000491375.1",
          "protein_id": null,
          "transcript_support_level": 5,
          "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": "retained_intron",
          "feature": "ENST00000491375.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AP5Z1",
          "gene_hgnc_id": 22197,
          "hgvs_c": "n.456C>A",
          "hgvs_p": null,
          "transcript": "ENST00000496303.6",
          "protein_id": null,
          "transcript_support_level": 2,
          "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,
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        {
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        {
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          "gene_symbol": "AP5Z1",
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          "hgvs_c": "n.721C>A",
          "hgvs_p": null,
          "transcript": "NR_157345.1",
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          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "pseudogene",
          "feature": "NR_157345.1"
        }
      ],
      "gene_symbol": "AP5Z1",
      "gene_hgnc_id": 22197,
      "dbsnp": "rs773542837",
      "frequency_reference_population": 7.000928e-7,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 1,
      "gnomad_exomes_af": 7.00093e-7,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 1,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.7091323733329773,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.248,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.104,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.23,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 4.657,
      "phylop100way_prediction": "Uncertain_significance",
      "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": 2,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2",
      "acmg_by_gene": [
        {
          "score": 2,
          "benign_score": 0,
          "pathogenic_score": 2,
          "criteria": [
            "PM2"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_014855.3",
          "gene_symbol": "AP5Z1",
          "hgnc_id": 22197,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.628C>A",
          "hgvs_p": "p.Pro210Thr"
        }
      ],
      "clinvar_disease": "Hereditary spastic paraplegia 48",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "Hereditary spastic paraplegia 48",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}