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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: 19-14413109-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=14413109&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "19",
      "pos": 14413109,
      "ref": "A",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "NM_005804.4",
      "consequences": [
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "NM_005804.4",
          "protein_id": "NP_005795.2",
          "transcript_support_level": null,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 427,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 1284,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000242776.9",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_005804.4"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000242776.9",
          "protein_id": "ENSP00000242776.3",
          "transcript_support_level": 1,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 427,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 1284,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_005804.4",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000242776.9"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "n.112T>C",
          "hgvs_p": null,
          "transcript": "ENST00000324340.13",
          "protein_id": "ENSP00000322749.8",
          "transcript_support_level": 1,
          "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": "nonsense_mediated_decay",
          "feature": "ENST00000324340.13"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "n.184T>C",
          "hgvs_p": null,
          "transcript": "ENST00000589318.5",
          "protein_id": null,
          "transcript_support_level": 1,
          "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": "ENST00000589318.5"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000926037.1",
          "protein_id": "ENSP00000596096.1",
          "transcript_support_level": null,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 435,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 1308,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000926037.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000898540.1",
          "protein_id": "ENSP00000568599.1",
          "transcript_support_level": null,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 427,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 1284,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000898540.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000926035.1",
          "protein_id": "ENSP00000596094.1",
          "transcript_support_level": null,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 427,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 1284,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000926035.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000926036.1",
          "protein_id": "ENSP00000596095.1",
          "transcript_support_level": null,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 427,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 1284,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000926036.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000926039.1",
          "protein_id": "ENSP00000596098.1",
          "transcript_support_level": null,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 427,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 1284,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000926039.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000950771.1",
          "protein_id": "ENSP00000620830.1",
          "transcript_support_level": null,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 427,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 1284,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000950771.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000898538.1",
          "protein_id": "ENSP00000568597.1",
          "transcript_support_level": null,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 416,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 1251,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000898538.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000898539.1",
          "protein_id": "ENSP00000568598.1",
          "transcript_support_level": null,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 383,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 1152,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000898539.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000926038.1",
          "protein_id": "ENSP00000596097.1",
          "transcript_support_level": null,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 326,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 981,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000926038.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000454233.6",
          "protein_id": "ENSP00000392929.2",
          "transcript_support_level": 3,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 267,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 804,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000454233.6"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000589675.5",
          "protein_id": "ENSP00000467911.1",
          "transcript_support_level": 3,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 254,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 765,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000589675.5"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.73T>C",
          "hgvs_p": "p.Tyr25His",
          "transcript": "ENST00000590315.5",
          "protein_id": "ENSP00000467411.1",
          "transcript_support_level": 5,
          "aa_start": 25,
          "aa_end": null,
          "aa_length": 187,
          "cds_start": 73,
          "cds_end": null,
          "cds_length": 565,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000590315.5"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000590239.5",
          "protein_id": "ENSP00000466810.1",
          "transcript_support_level": 4,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 129,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 392,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000590239.5"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000586993.5",
          "protein_id": "ENSP00000464801.1",
          "transcript_support_level": 4,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 124,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 375,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000586993.5"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000591275.5",
          "protein_id": "ENSP00000465926.1",
          "transcript_support_level": 2,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 107,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 325,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000591275.5"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His",
          "transcript": "ENST00000590696.1",
          "protein_id": "ENSP00000467040.1",
          "transcript_support_level": 4,
          "aa_start": 38,
          "aa_end": null,
          "aa_length": 91,
          "cds_start": 112,
          "cds_end": null,
          "cds_length": 277,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
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        },
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        {
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          "consequences": [
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          "hgvs_c": "n.188T>C",
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          "transcript": "ENST00000593008.1",
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          "biotype": "pseudogene",
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        {
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          "consequences": [
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          "exon_count": 10,
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          "gene_symbol": "DDX39A",
          "gene_hgnc_id": 17821,
          "hgvs_c": "n.230T>C",
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          "transcript": "NR_046366.2",
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "pseudogene",
          "feature": "NR_046366.2"
        }
      ],
      "gene_symbol": "DDX39A",
      "gene_hgnc_id": 17821,
      "dbsnp": null,
      "frequency_reference_population": null,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 0,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.5415439009666443,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.315,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.8538,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.11,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 8.401,
      "phylop100way_prediction": "Pathogenic",
      "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": 3,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,PP2",
      "acmg_by_gene": [
        {
          "score": 3,
          "benign_score": 0,
          "pathogenic_score": 3,
          "criteria": [
            "PM2",
            "PP2"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_005804.4",
          "gene_symbol": "DDX39A",
          "hgnc_id": 17821,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.112T>C",
          "hgvs_p": "p.Tyr38His"
        }
      ],
      "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
}