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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: 3-49026539-A-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49026539&ref=A&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 49026539,
      "ref": "A",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "NM_001410759.1",
      "consequences": [
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.890T>A",
          "hgvs_p": "p.Leu297His",
          "transcript": "NM_000884.3",
          "protein_id": "NP_000875.2",
          "transcript_support_level": null,
          "aa_start": 297,
          "aa_end": null,
          "aa_length": 514,
          "cds_start": 890,
          "cds_end": null,
          "cds_length": 1545,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000326739.9",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_000884.3"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.890T>A",
          "hgvs_p": "p.Leu297His",
          "transcript": "ENST00000326739.9",
          "protein_id": "ENSP00000321584.4",
          "transcript_support_level": 1,
          "aa_start": 297,
          "aa_end": null,
          "aa_length": 514,
          "cds_start": 890,
          "cds_end": null,
          "cds_length": 1545,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_000884.3",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000326739.9"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000290315",
          "gene_hgnc_id": null,
          "hgvs_c": "c.2930T>A",
          "hgvs_p": "p.Leu977His",
          "transcript": "ENST00000703936.1",
          "protein_id": "ENSP00000515567.1",
          "transcript_support_level": null,
          "aa_start": 977,
          "aa_end": null,
          "aa_length": 1194,
          "cds_start": 2930,
          "cds_end": null,
          "cds_length": 3585,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000703936.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.1058T>A",
          "hgvs_p": "p.Leu353His",
          "transcript": "ENST00000937815.1",
          "protein_id": "ENSP00000607874.1",
          "transcript_support_level": null,
          "aa_start": 353,
          "aa_end": null,
          "aa_length": 570,
          "cds_start": 1058,
          "cds_end": null,
          "cds_length": 1713,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000937815.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.890T>A",
          "hgvs_p": "p.Leu297His",
          "transcript": "NM_001410759.1",
          "protein_id": "NP_001397688.1",
          "transcript_support_level": null,
          "aa_start": 297,
          "aa_end": null,
          "aa_length": 538,
          "cds_start": 890,
          "cds_end": null,
          "cds_length": 1617,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001410759.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.890T>A",
          "hgvs_p": "p.Leu297His",
          "transcript": "ENST00000429182.6",
          "protein_id": "ENSP00000393525.2",
          "transcript_support_level": 5,
          "aa_start": 297,
          "aa_end": null,
          "aa_length": 538,
          "cds_start": 890,
          "cds_end": null,
          "cds_length": 1617,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000429182.6"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.887T>A",
          "hgvs_p": "p.Leu296His",
          "transcript": "ENST00000968719.1",
          "protein_id": "ENSP00000638778.1",
          "transcript_support_level": null,
          "aa_start": 296,
          "aa_end": null,
          "aa_length": 537,
          "cds_start": 887,
          "cds_end": null,
          "cds_length": 1614,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000968719.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.878T>A",
          "hgvs_p": "p.Leu293His",
          "transcript": "ENST00000968723.1",
          "protein_id": "ENSP00000638782.1",
          "transcript_support_level": null,
          "aa_start": 293,
          "aa_end": null,
          "aa_length": 534,
          "cds_start": 878,
          "cds_end": null,
          "cds_length": 1605,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000968723.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.866T>A",
          "hgvs_p": "p.Leu289His",
          "transcript": "ENST00000937818.1",
          "protein_id": "ENSP00000607877.1",
          "transcript_support_level": null,
          "aa_start": 289,
          "aa_end": null,
          "aa_length": 530,
          "cds_start": 866,
          "cds_end": null,
          "cds_length": 1593,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000937818.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.926T>A",
          "hgvs_p": "p.Leu309His",
          "transcript": "ENST00000937813.1",
          "protein_id": "ENSP00000607872.1",
          "transcript_support_level": null,
          "aa_start": 309,
          "aa_end": null,
          "aa_length": 526,
          "cds_start": 926,
          "cds_end": null,
          "cds_length": 1581,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000937813.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.914T>A",
          "hgvs_p": "p.Leu305His",
          "transcript": "ENST00000677010.1",
          "protein_id": "ENSP00000503089.1",
          "transcript_support_level": null,
          "aa_start": 305,
          "aa_end": null,
          "aa_length": 522,
          "cds_start": 914,
          "cds_end": null,
          "cds_length": 1569,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000677010.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.890T>A",
          "hgvs_p": "p.Leu297His",
          "transcript": "ENST00000881196.1",
          "protein_id": "ENSP00000551255.1",
          "transcript_support_level": null,
          "aa_start": 297,
          "aa_end": null,
          "aa_length": 520,
          "cds_start": 890,
          "cds_end": null,
          "cds_length": 1563,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000881196.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.833T>A",
          "hgvs_p": "p.Leu278His",
          "transcript": "ENST00000881195.1",
          "protein_id": "ENSP00000551254.1",
          "transcript_support_level": null,
          "aa_start": 278,
          "aa_end": null,
          "aa_length": 519,
          "cds_start": 833,
          "cds_end": null,
          "cds_length": 1560,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000881195.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.890T>A",
          "hgvs_p": "p.Leu297His",
          "transcript": "ENST00000968724.1",
          "protein_id": "ENSP00000638783.1",
          "transcript_support_level": null,
          "aa_start": 297,
          "aa_end": null,
          "aa_length": 519,
          "cds_start": 890,
          "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": "L",
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 7,
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          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.815T>A",
          "hgvs_p": "p.Leu272His",
          "transcript": "NM_001410760.1",
          "protein_id": "NP_001397689.1",
          "transcript_support_level": null,
          "aa_start": 272,
          "aa_end": null,
          "aa_length": 513,
          "cds_start": 815,
          "cds_end": null,
          "cds_length": 1542,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001410760.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.815T>A",
          "hgvs_p": "p.Leu272His",
          "transcript": "ENST00000678724.1",
          "protein_id": "ENSP00000503874.1",
          "transcript_support_level": null,
          "aa_start": 272,
          "aa_end": null,
          "aa_length": 513,
          "cds_start": 815,
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          "cds_length": 1542,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000678724.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.887T>A",
          "hgvs_p": "p.Leu296His",
          "transcript": "ENST00000937811.1",
          "protein_id": "ENSP00000607870.1",
          "transcript_support_level": null,
          "aa_start": 296,
          "aa_end": null,
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          "cds_start": 887,
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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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        },
        {
          "aa_ref": "L",
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
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          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.890T>A",
          "hgvs_p": "p.Leu297His",
          "transcript": "ENST00000937820.1",
          "protein_id": "ENSP00000607879.1",
          "transcript_support_level": null,
          "aa_start": 297,
          "aa_end": null,
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          "cds_start": 890,
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          "cds_length": 1542,
          "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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          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
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          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.884T>A",
          "hgvs_p": "p.Leu295His",
          "transcript": "ENST00000937810.1",
          "protein_id": "ENSP00000607869.1",
          "transcript_support_level": null,
          "aa_start": 295,
          "aa_end": null,
          "aa_length": 512,
          "cds_start": 884,
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          "cds_length": 1539,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000937810.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IMPDH2",
          "gene_hgnc_id": 6053,
          "hgvs_c": "c.884T>A",
          "hgvs_p": "p.Leu295His",
          "transcript": "ENST00000937817.1",
          "protein_id": "ENSP00000607876.1",
          "transcript_support_level": null,
          "aa_start": 295,
          "aa_end": null,
          "aa_length": 512,
          "cds_start": 884,
          "cds_end": null,
          "cds_length": 1539,
          "cdna_start": null,
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        {
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        {
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          "consequences": [
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          "gene_symbol": "ENSG00000290315",
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          "transcript": "ENST00000703937.1",
          "protein_id": "ENSP00000515568.1",
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          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000703937.1"
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      ],
      "gene_symbol": "IMPDH2",
      "gene_hgnc_id": 6053,
      "dbsnp": null,
      "frequency_reference_population": 0.0000013685844,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 2,
      "gnomad_exomes_af": 0.00000136858,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 2,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.9257590174674988,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.798,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.8141,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.19,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 9.206,
      "phylop100way_prediction": "Pathogenic",
      "spliceai_max_score": 0.01,
      "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": 5,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,PP2,PP3_Moderate",
      "acmg_by_gene": [
        {
          "score": 5,
          "benign_score": 0,
          "pathogenic_score": 5,
          "criteria": [
            "PM2",
            "PP2",
            "PP3_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_001410759.1",
          "gene_symbol": "IMPDH2",
          "hgnc_id": 6053,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.890T>A",
          "hgvs_p": "p.Leu297His"
        },
        {
          "score": 4,
          "benign_score": 0,
          "pathogenic_score": 4,
          "criteria": [
            "PM2",
            "PP3_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000703936.1",
          "gene_symbol": "ENSG00000290315",
          "hgnc_id": null,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.2930T>A",
          "hgvs_p": "p.Leu977His"
        }
      ],
      "clinvar_disease": "not provided",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "not provided",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}