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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: 1-13778502-C-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=13778502&ref=C&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 13778502,
      "ref": "C",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "NM_012231.5",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.707C>G",
          "hgvs_p": "p.Pro236Arg",
          "transcript": "NM_001393986.1",
          "protein_id": "NP_001380915.1",
          "transcript_support_level": null,
          "aa_start": 236,
          "aa_end": null,
          "aa_length": 1718,
          "cds_start": 707,
          "cds_end": null,
          "cds_length": 5157,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000311066.10",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001393986.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.707C>G",
          "hgvs_p": "p.Pro236Arg",
          "transcript": "ENST00000311066.10",
          "protein_id": "ENSP00000312352.6",
          "transcript_support_level": 5,
          "aa_start": 236,
          "aa_end": null,
          "aa_length": 1718,
          "cds_start": 707,
          "cds_end": null,
          "cds_length": 5157,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_001393986.1",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000311066.10"
        },
        {
          "aa_ref": "P",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.707C>G",
          "hgvs_p": "p.Pro236Arg",
          "transcript": "ENST00000235372.11",
          "protein_id": "ENSP00000235372.6",
          "transcript_support_level": 1,
          "aa_start": 236,
          "aa_end": null,
          "aa_length": 1718,
          "cds_start": 707,
          "cds_end": null,
          "cds_length": 5157,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000235372.11"
        },
        {
          "aa_ref": "P",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.104C>G",
          "hgvs_p": "p.Pro35Arg",
          "transcript": "ENST00000343137.8",
          "protein_id": "ENSP00000341621.4",
          "transcript_support_level": 1,
          "aa_start": 35,
          "aa_end": null,
          "aa_length": 1481,
          "cds_start": 104,
          "cds_end": null,
          "cds_length": 4446,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000343137.8"
        },
        {
          "aa_ref": "P",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.104C>G",
          "hgvs_p": "p.Pro35Arg",
          "transcript": "ENST00000413440.5",
          "protein_id": "ENSP00000411103.1",
          "transcript_support_level": 1,
          "aa_start": 35,
          "aa_end": null,
          "aa_length": 1481,
          "cds_start": 104,
          "cds_end": null,
          "cds_length": 4446,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000413440.5"
        },
        {
          "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": 5,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.19+5314C>G",
          "hgvs_p": null,
          "transcript": "ENST00000503842.5",
          "protein_id": "ENSP00000425028.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 62,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 189,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000503842.5"
        },
        {
          "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": 4,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.19+5314C>G",
          "hgvs_p": null,
          "transcript": "ENST00000505823.5",
          "protein_id": "ENSP00000426737.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 62,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 189,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000505823.5"
        },
        {
          "aa_ref": "P",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.707C>G",
          "hgvs_p": "p.Pro236Arg",
          "transcript": "NM_012231.5",
          "protein_id": "NP_036363.2",
          "transcript_support_level": null,
          "aa_start": 236,
          "aa_end": null,
          "aa_length": 1718,
          "cds_start": 707,
          "cds_end": null,
          "cds_length": 5157,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_012231.5"
        },
        {
          "aa_ref": "P",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.707C>G",
          "hgvs_p": "p.Pro236Arg",
          "transcript": "NM_015866.6",
          "protein_id": "NP_056950.2",
          "transcript_support_level": null,
          "aa_start": 236,
          "aa_end": null,
          "aa_length": 1682,
          "cds_start": 707,
          "cds_end": null,
          "cds_length": 5049,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_015866.6"
        },
        {
          "aa_ref": "P",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.104C>G",
          "hgvs_p": "p.Pro35Arg",
          "transcript": "NM_001393987.1",
          "protein_id": "NP_001380916.1",
          "transcript_support_level": null,
          "aa_start": 35,
          "aa_end": null,
          "aa_length": 1517,
          "cds_start": 104,
          "cds_end": null,
          "cds_length": 4554,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001393987.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.104C>G",
          "hgvs_p": "p.Pro35Arg",
          "transcript": "NM_001007257.3",
          "protein_id": "NP_001007258.1",
          "transcript_support_level": null,
          "aa_start": 35,
          "aa_end": null,
          "aa_length": 1481,
          "cds_start": 104,
          "cds_end": null,
          "cds_length": 4446,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001007257.3"
        },
        {
          "aa_ref": "P",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.104C>G",
          "hgvs_p": "p.Pro35Arg",
          "transcript": "NM_001393988.1",
          "protein_id": "NP_001380917.1",
          "transcript_support_level": null,
          "aa_start": 35,
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          "aa_length": 1481,
          "cds_start": 104,
          "cds_end": null,
          "cds_length": 4446,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001393988.1"
        },
        {
          "aa_ref": "P",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.104C>G",
          "hgvs_p": "p.Pro35Arg",
          "transcript": "ENST00000407521.7",
          "protein_id": "ENSP00000384430.3",
          "transcript_support_level": 4,
          "aa_start": 35,
          "aa_end": null,
          "aa_length": 77,
          "cds_start": 104,
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          "cds_length": 234,
          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000407521.7"
        },
        {
          "aa_ref": "P",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.704C>G",
          "hgvs_p": "p.Pro235Arg",
          "transcript": "XM_047429996.1",
          "protein_id": "XP_047285952.1",
          "transcript_support_level": null,
          "aa_start": 235,
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          "aa_length": 1717,
          "cds_start": 704,
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          "cdna_start": null,
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          "cdna_length": null,
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          "biotype": "protein_coding",
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        },
        {
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          "strand": true,
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          ],
          "exon_rank": 7,
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          "exon_count": 8,
          "intron_rank": null,
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          "gene_symbol": "PRDM2",
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          "hgvs_c": "c.485C>G",
          "hgvs_p": "p.Pro162Arg",
          "transcript": "XM_047429994.1",
          "protein_id": "XP_047285950.1",
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          "cds_start": 485,
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          "cds_length": 4935,
          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "XM_047429994.1"
        },
        {
          "aa_ref": "P",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
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          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.485C>G",
          "hgvs_p": "p.Pro162Arg",
          "transcript": "XM_047429995.1",
          "protein_id": "XP_047285951.1",
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          "aa_start": 162,
          "aa_end": null,
          "aa_length": 1608,
          "cds_start": 485,
          "cds_end": null,
          "cds_length": 4827,
          "cdna_start": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "P",
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.104C>G",
          "hgvs_p": "p.Pro35Arg",
          "transcript": "XM_017002260.3",
          "protein_id": "XP_016857749.1",
          "transcript_support_level": null,
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        {
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          "intron_rank": null,
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          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
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          "transcript": "XM_017002261.3",
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        },
        {
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          "gene_symbol": "PRDM2",
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          "hgvs_c": "c.104C>G",
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        },
        {
          "aa_ref": "P",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
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          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.104C>G",
          "hgvs_p": "p.Pro35Arg",
          "transcript": "XM_047429998.1",
          "protein_id": "XP_047285954.1",
          "transcript_support_level": null,
          "aa_start": 35,
          "aa_end": null,
          "aa_length": 1481,
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          "cdna_start": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.511+29015C>G",
          "hgvs_p": null,
          "transcript": "NM_001135610.2",
          "protein_id": "NP_001129082.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 226,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 681,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001135610.2"
        },
        {
          "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": 8,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.511+29015C>G",
          "hgvs_p": null,
          "transcript": "ENST00000376048.9",
          "protein_id": "ENSP00000365216.5",
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 226,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 681,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000376048.9"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "n.*412+5314C>G",
          "hgvs_p": null,
          "transcript": "ENST00000491134.5",
          "protein_id": "ENSP00000424253.1",
          "transcript_support_level": 3,
          "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": "ENST00000491134.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRDM2",
          "gene_hgnc_id": 9347,
          "hgvs_c": "c.*39C>G",
          "hgvs_p": null,
          "transcript": "ENST00000487453.1",
          "protein_id": "ENSP00000474273.1",
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 20,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 65,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000487453.1"
        }
      ],
      "gene_symbol": "PRDM2",
      "gene_hgnc_id": 9347,
      "dbsnp": "rs371186158",
      "frequency_reference_population": 0.000003717366,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 6,
      "gnomad_exomes_af": 0.00000136809,
      "gnomad_genomes_af": 0.0000262885,
      "gnomad_exomes_ac": 2,
      "gnomad_genomes_ac": 4,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.05369320511817932,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.019999999552965164,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.111,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0808,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.68,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.109,
      "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": -4,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4_Strong",
      "acmg_by_gene": [
        {
          "score": -4,
          "benign_score": 4,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_012231.5",
          "gene_symbol": "PRDM2",
          "hgnc_id": 9347,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.707C>G",
          "hgvs_p": "p.Pro236Arg"
        }
      ],
      "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
}