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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: 7-35873749-A-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=35873749&ref=A&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "7",
      "pos": 35873749,
      "ref": "A",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "NM_001788.6",
      "consequences": [
        {
          "aa_ref": "L",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.486A>T",
          "hgvs_p": "p.Leu162Phe",
          "transcript": "NM_001788.6",
          "protein_id": "NP_001779.3",
          "transcript_support_level": null,
          "aa_start": 162,
          "aa_end": null,
          "aa_length": 437,
          "cds_start": 486,
          "cds_end": null,
          "cds_length": 1314,
          "cdna_start": 639,
          "cdna_end": null,
          "cdna_length": 4284,
          "mane_select": "ENST00000350320.11",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "F",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.486A>T",
          "hgvs_p": "p.Leu162Phe",
          "transcript": "ENST00000350320.11",
          "protein_id": "ENSP00000344868.8",
          "transcript_support_level": 5,
          "aa_start": 162,
          "aa_end": null,
          "aa_length": 437,
          "cds_start": 486,
          "cds_end": null,
          "cds_length": 1314,
          "cdna_start": 639,
          "cdna_end": null,
          "cdna_length": 4284,
          "mane_select": "NM_001788.6",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "F",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.327A>T",
          "hgvs_p": "p.Leu109Phe",
          "transcript": "ENST00000635047.1",
          "protein_id": "ENSP00000489480.1",
          "transcript_support_level": 4,
          "aa_start": 109,
          "aa_end": null,
          "aa_length": 156,
          "cds_start": 327,
          "cds_end": null,
          "cds_length": 471,
          "cdna_start": 616,
          "cdna_end": null,
          "cdna_length": 760,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "n.*403A>T",
          "hgvs_p": null,
          "transcript": "ENST00000635175.1",
          "protein_id": "ENSP00000489192.1",
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1464,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "n.*403A>T",
          "hgvs_p": null,
          "transcript": "ENST00000635175.1",
          "protein_id": "ENSP00000489192.1",
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1464,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.483A>T",
          "hgvs_p": "p.Leu161Phe",
          "transcript": "NM_001011553.4",
          "protein_id": "NP_001011553.2",
          "transcript_support_level": null,
          "aa_start": 161,
          "aa_end": null,
          "aa_length": 436,
          "cds_start": 483,
          "cds_end": null,
          "cds_length": 1311,
          "cdna_start": 636,
          "cdna_end": null,
          "cdna_length": 2478,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.483A>T",
          "hgvs_p": "p.Leu161Phe",
          "transcript": "ENST00000705486.1",
          "protein_id": "ENSP00000516132.1",
          "transcript_support_level": null,
          "aa_start": 161,
          "aa_end": null,
          "aa_length": 436,
          "cds_start": 483,
          "cds_end": null,
          "cds_length": 1311,
          "cdna_start": 507,
          "cdna_end": null,
          "cdna_length": 2349,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.426A>T",
          "hgvs_p": "p.Leu142Phe",
          "transcript": "ENST00000399035.7",
          "protein_id": "ENSP00000381993.4",
          "transcript_support_level": 5,
          "aa_start": 142,
          "aa_end": null,
          "aa_length": 417,
          "cds_start": 426,
          "cds_end": null,
          "cds_length": 1254,
          "cdna_start": 426,
          "cdna_end": null,
          "cdna_length": 4066,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.378A>T",
          "hgvs_p": "p.Leu126Phe",
          "transcript": "NM_001242956.1",
          "protein_id": "NP_001229885.1",
          "transcript_support_level": null,
          "aa_start": 126,
          "aa_end": null,
          "aa_length": 401,
          "cds_start": 378,
          "cds_end": null,
          "cds_length": 1206,
          "cdna_start": 602,
          "cdna_end": null,
          "cdna_length": 4242,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.378A>T",
          "hgvs_p": "p.Leu126Phe",
          "transcript": "ENST00000435235.6",
          "protein_id": "ENSP00000413507.2",
          "transcript_support_level": 2,
          "aa_start": 126,
          "aa_end": null,
          "aa_length": 401,
          "cds_start": 378,
          "cds_end": null,
          "cds_length": 1206,
          "cdna_start": 549,
          "cdna_end": null,
          "cdna_length": 1584,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.327A>T",
          "hgvs_p": "p.Leu109Phe",
          "transcript": "NM_001363715.2",
          "protein_id": "NP_001350644.1",
          "transcript_support_level": null,
          "aa_start": 109,
          "aa_end": null,
          "aa_length": 384,
          "cds_start": 327,
          "cds_end": null,
          "cds_length": 1155,
          "cdna_start": 1015,
          "cdna_end": null,
          "cdna_length": 4660,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.327A>T",
          "hgvs_p": "p.Leu109Phe",
          "transcript": "NM_001375299.1",
          "protein_id": "NP_001362228.1",
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          "aa_start": 109,
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          "aa_length": 384,
          "cds_start": 327,
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          "cdna_start": 472,
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          "cdna_length": 2314,
          "mane_select": null,
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          "biotype": null,
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        },
        {
          "aa_ref": "L",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
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          "exon_count": 13,
          "intron_rank": null,
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          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.327A>T",
          "hgvs_p": "p.Leu109Phe",
          "transcript": "ENST00000399034.7",
          "protein_id": "ENSP00000381992.4",
          "transcript_support_level": 5,
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          "cds_start": 327,
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          "cdna_start": 759,
          "cdna_end": null,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
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          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.486A>T",
          "hgvs_p": "p.Leu162Phe",
          "transcript": "ENST00000672279.1",
          "protein_id": "ENSP00000499937.1",
          "transcript_support_level": null,
          "aa_start": 162,
          "aa_end": null,
          "aa_length": 174,
          "cds_start": 486,
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          "cds_length": 525,
          "cdna_start": 510,
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          "cdna_length": 3095,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
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        },
        {
          "aa_ref": "L",
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          "consequences": [
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          ],
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          "intron_rank": null,
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          "gene_symbol": "SEPTIN7",
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          "hgvs_c": "c.327A>T",
          "hgvs_p": "p.Leu109Phe",
          "transcript": "ENST00000634600.1",
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          "cdna_start": 469,
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          "mane_select": null,
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          "biotype": null,
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        {
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 6,
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          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.486A>T",
          "hgvs_p": "p.Leu162Phe",
          "transcript": "XM_011515656.3",
          "protein_id": "XP_011513958.1",
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          "aa_end": null,
          "aa_length": 460,
          "cds_start": 486,
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          "cds_length": 1383,
          "cdna_start": 639,
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          "cdna_length": 1551,
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        {
          "aa_ref": "L",
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          "canonical": false,
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 6,
          "exon_rank_end": null,
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          "intron_rank": null,
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          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.486A>T",
          "hgvs_p": "p.Leu162Phe",
          "transcript": "XM_006715806.4",
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          "cdna_start": 639,
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        },
        {
          "aa_ref": "L",
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          "protein_coding": true,
          "strand": true,
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          ],
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          "intron_rank": null,
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          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.486A>T",
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        },
        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "SEPTIN7",
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          "hgvs_c": "c.483A>T",
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          "transcript": "XM_047421095.1",
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        },
        {
          "aa_ref": "L",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
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          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
          "hgvs_c": "c.396A>T",
          "hgvs_p": "p.Leu132Phe",
          "transcript": "XM_047421096.1",
          "protein_id": "XP_047277052.1",
          "transcript_support_level": null,
          "aa_start": 132,
          "aa_end": null,
          "aa_length": 407,
          "cds_start": 396,
          "cds_end": null,
          "cds_length": 1224,
          "cdna_start": 412,
          "cdna_end": null,
          "cdna_length": 4057,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SEPTIN7",
          "gene_hgnc_id": 1717,
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          "hgvs_p": "p.Leu109Phe",
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          "gene_symbol": "SEPTIN7",
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        },
        {
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          "gene_symbol": "SEPTIN7",
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        },
        {
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          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
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          "exon_count": 6,
          "intron_rank": null,
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          "gene_symbol": "SEPTIN7",
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          "hgvs_c": "n.505A>T",
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          "transcript": "ENST00000635420.1",
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          "transcript_support_level": 3,
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          "cdna_length": 581,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "SEPTIN7",
      "gene_hgnc_id": 1717,
      "dbsnp": "rs755357863",
      "frequency_reference_population": 0.00005588174,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 90,
      "gnomad_exomes_af": 0.0000589678,
      "gnomad_genomes_af": 0.000026295,
      "gnomad_exomes_ac": 86,
      "gnomad_genomes_ac": 4,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.6783596873283386,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.019999999552965164,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.562,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.7947,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.06,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 0.399,
      "phylop100way_prediction": "Benign",
      "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": "Uncertain_significance",
      "acmg_criteria": "PM2",
      "acmg_by_gene": [
        {
          "score": 2,
          "benign_score": 0,
          "pathogenic_score": 2,
          "criteria": [
            "PM2"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_001788.6",
          "gene_symbol": "SEPTIN7",
          "hgnc_id": 1717,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.486A>T",
          "hgvs_p": "p.Leu162Phe"
        }
      ],
      "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
}