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GeneBe API Showcase

This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.

API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.

Documentation & Advanced Usage

Complete API documentation:docs.genebe.net/docs/api/overview/

Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/

Python client for pandas:pypi.org/project/genebe/

Java CLI for VCF files:github.com/pstawinski/genebe-cli

All tools documented at:docs.genebe.net

API Request Examples for Variant: 4-120695145-TG-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=120695145&ref=TG&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "4",
      "pos": 120695145,
      "ref": "TG",
      "alt": "T",
      "effect": "frameshift_variant",
      "transcript": "NM_001379104.1",
      "consequences": [
        {
          "aa_ref": "H",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1858delC",
          "hgvs_p": "p.His620fs",
          "transcript": "NM_018699.4",
          "protein_id": "NP_061169.2",
          "transcript_support_level": null,
          "aa_start": 620,
          "aa_end": null,
          "aa_length": 630,
          "cds_start": 1858,
          "cds_end": null,
          "cds_length": 1893,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000264808.8",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_018699.4"
        },
        {
          "aa_ref": "H",
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1858delC",
          "hgvs_p": "p.His620fs",
          "transcript": "ENST00000264808.8",
          "protein_id": "ENSP00000264808.3",
          "transcript_support_level": 1,
          "aa_start": 620,
          "aa_end": null,
          "aa_length": 630,
          "cds_start": 1858,
          "cds_end": null,
          "cds_length": 1893,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_018699.4",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000264808.8"
        },
        {
          "aa_ref": "H",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1765delC",
          "hgvs_p": "p.His589fs",
          "transcript": "ENST00000428209.6",
          "protein_id": "ENSP00000404832.2",
          "transcript_support_level": 1,
          "aa_start": 589,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 1765,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000428209.6"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.*173delC",
          "hgvs_p": null,
          "transcript": "ENST00000515109.5",
          "protein_id": "ENSP00000422309.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 501,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1506,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000515109.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "n.2361delC",
          "hgvs_p": null,
          "transcript": "ENST00000505484.5",
          "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": "ENST00000505484.5"
        },
        {
          "aa_ref": "H",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1891delC",
          "hgvs_p": "p.His631fs",
          "transcript": "NM_001379104.1",
          "protein_id": "NP_001366033.1",
          "transcript_support_level": null,
          "aa_start": 631,
          "aa_end": null,
          "aa_length": 641,
          "cds_start": 1891,
          "cds_end": null,
          "cds_length": 1926,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001379104.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1891delC",
          "hgvs_p": "p.His631fs",
          "transcript": "ENST00000940463.1",
          "protein_id": "ENSP00000610522.1",
          "transcript_support_level": null,
          "aa_start": 631,
          "aa_end": null,
          "aa_length": 641,
          "cds_start": 1891,
          "cds_end": null,
          "cds_length": 1926,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000940463.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1798delC",
          "hgvs_p": "p.His600fs",
          "transcript": "ENST00000940462.1",
          "protein_id": "ENSP00000610521.1",
          "transcript_support_level": null,
          "aa_start": 600,
          "aa_end": null,
          "aa_length": 610,
          "cds_start": 1798,
          "cds_end": null,
          "cds_length": 1833,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000940462.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1765delC",
          "hgvs_p": "p.His589fs",
          "transcript": "NM_001300823.2",
          "protein_id": "NP_001287752.1",
          "transcript_support_level": null,
          "aa_start": 589,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 1765,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001300823.2"
        },
        {
          "aa_ref": "H",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1753delC",
          "hgvs_p": "p.His585fs",
          "transcript": "ENST00000898038.1",
          "protein_id": "ENSP00000568097.1",
          "transcript_support_level": null,
          "aa_start": 585,
          "aa_end": null,
          "aa_length": 595,
          "cds_start": 1753,
          "cds_end": null,
          "cds_length": 1788,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000898038.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1681delC",
          "hgvs_p": "p.His561fs",
          "transcript": "ENST00000898039.1",
          "protein_id": "ENSP00000568098.1",
          "transcript_support_level": null,
          "aa_start": 561,
          "aa_end": null,
          "aa_length": 571,
          "cds_start": 1681,
          "cds_end": null,
          "cds_length": 1716,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000898039.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1660delC",
          "hgvs_p": "p.His554fs",
          "transcript": "NM_001379106.1",
          "protein_id": "NP_001366035.1",
          "transcript_support_level": null,
          "aa_start": 554,
          "aa_end": null,
          "aa_length": 564,
          "cds_start": 1660,
          "cds_end": null,
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          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
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        {
          "aa_ref": "H",
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          "canonical": false,
          "protein_coding": true,
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          ],
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          "exon_count": 14,
          "intron_rank": null,
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          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1660delC",
          "hgvs_p": "p.His554fs",
          "transcript": "ENST00000940461.1",
          "protein_id": "ENSP00000610520.1",
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          "cds_start": 1660,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "H",
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          "canonical": false,
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1813delC",
          "hgvs_p": "p.His605fs",
          "transcript": "XM_017007668.3",
          "protein_id": "XP_016863157.1",
          "transcript_support_level": null,
          "aa_start": 605,
          "aa_end": null,
          "aa_length": 615,
          "cds_start": 1813,
          "cds_end": null,
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          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
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        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
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          "hgvs_p": "p.His600fs",
          "transcript": "XM_011531563.3",
          "protein_id": "XP_011529865.1",
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          "aa_start": 600,
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          "cdna_start": null,
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          "biotype": "protein_coding",
          "feature": "XM_011531563.3"
        },
        {
          "aa_ref": "H",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1786delC",
          "hgvs_p": "p.His596fs",
          "transcript": "XM_011531564.3",
          "protein_id": "XP_011529866.1",
          "transcript_support_level": null,
          "aa_start": 596,
          "aa_end": null,
          "aa_length": 606,
          "cds_start": 1786,
          "cds_end": null,
          "cds_length": 1821,
          "cdna_start": null,
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          "cdna_length": null,
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          "biotype": "protein_coding",
          "feature": "XM_011531564.3"
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        {
          "aa_ref": "H",
          "aa_alt": null,
          "canonical": false,
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1753delC",
          "hgvs_p": "p.His585fs",
          "transcript": "XM_047449554.1",
          "protein_id": "XP_047305510.1",
          "transcript_support_level": null,
          "aa_start": 585,
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          "cds_start": 1753,
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          "cdna_start": null,
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        {
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          ],
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          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.916delC",
          "hgvs_p": "p.His306fs",
          "transcript": "XM_017007671.2",
          "protein_id": "XP_016863160.1",
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          "aa_end": null,
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          "cds_start": 916,
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          "cdna_start": null,
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          "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": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 14,
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          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.*173delC",
          "hgvs_p": null,
          "transcript": "NM_001300824.2",
          "protein_id": "NP_001287753.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": 501,
          "cds_start": null,
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          "cds_length": 1506,
          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "NM_001300824.2"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 15,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1762-10121delC",
          "hgvs_p": null,
          "transcript": "XM_011531566.4",
          "protein_id": "XP_011529868.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 589,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1770,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_011531566.4"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 14,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1669-10121delC",
          "hgvs_p": null,
          "transcript": "XM_047449557.1",
          "protein_id": "XP_047305513.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 558,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1677,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047449557.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 14,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "c.1636-10121delC",
          "hgvs_p": null,
          "transcript": "XM_047449558.1",
          "protein_id": "XP_047305514.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 547,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1644,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047449558.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "n.104-10121delC",
          "hgvs_p": null,
          "transcript": "ENST00000513741.1",
          "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": "pseudogene",
          "feature": "ENST00000513741.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM5",
          "gene_hgnc_id": 9349,
          "hgvs_c": "n.*12delC",
          "hgvs_p": null,
          "transcript": "ENST00000506065.1",
          "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": "pseudogene",
          "feature": "ENST00000506065.1"
        }
      ],
      "gene_symbol": "PRDM5",
      "gene_hgnc_id": 9349,
      "dbsnp": "rs1734373037",
      "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": null,
      "computational_prediction_selected": null,
      "computational_source_selected": null,
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": null,
      "bayesdelnoaf_prediction": null,
      "phylop100way_score": 9.411,
      "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": 6,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PVS1_Moderate,PM2,PP5_Moderate",
      "acmg_by_gene": [
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PVS1_Moderate",
            "PM2",
            "PP5_Moderate"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "NM_001379104.1",
          "gene_symbol": "PRDM5",
          "hgnc_id": 9349,
          "effects": [
            "frameshift_variant"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "c.1891delC",
          "hgvs_p": "p.His631fs"
        }
      ],
      "clinvar_disease": "Brittle cornea syndrome 2",
      "clinvar_classification": "Likely pathogenic",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "LP:1",
      "phenotype_combined": "Brittle cornea syndrome 2",
      "pathogenicity_classification_combined": "Likely pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}