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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: 10-53809138-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=53809138&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "10",
      "pos": 53809138,
      "ref": "A",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "NM_001142769.3",
      "consequences": [
        {
          "aa_ref": "S",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 35,
          "exon_rank_end": null,
          "exon_count": 35,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4906T>C",
          "hgvs_p": "p.Ser1636Pro",
          "transcript": "ENST00000395445.6",
          "protein_id": "ENSP00000378832.2",
          "transcript_support_level": 1,
          "aa_start": 1636,
          "aa_end": null,
          "aa_length": 1783,
          "cds_start": 4906,
          "cds_end": null,
          "cds_length": 5352,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000395445.6"
        },
        {
          "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": 38,
          "intron_rank": 37,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4671+1418T>C",
          "hgvs_p": null,
          "transcript": "NM_001384140.1",
          "protein_id": "NP_001371069.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1740,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 5223,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000644397.2",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001384140.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 38,
          "intron_rank": 37,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4671+1418T>C",
          "hgvs_p": null,
          "transcript": "ENST00000644397.2",
          "protein_id": "ENSP00000495195.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1740,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 5223,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_001384140.1",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000644397.2"
        },
        {
          "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": 34,
          "intron_rank": 33,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4476+1418T>C",
          "hgvs_p": null,
          "transcript": "ENST00000616114.4",
          "protein_id": "ENSP00000483745.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1675,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 5028,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000616114.4"
        },
        {
          "aa_ref": "S",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 37,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4927T>C",
          "hgvs_p": "p.Ser1643Pro",
          "transcript": "NM_001142769.3",
          "protein_id": "NP_001136241.1",
          "transcript_support_level": null,
          "aa_start": 1643,
          "aa_end": null,
          "aa_length": 1790,
          "cds_start": 4927,
          "cds_end": null,
          "cds_length": 5373,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001142769.3"
        },
        {
          "aa_ref": "S",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 37,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4927T>C",
          "hgvs_p": "p.Ser1643Pro",
          "transcript": "ENST00000613657.6",
          "protein_id": "ENSP00000482794.1",
          "transcript_support_level": 5,
          "aa_start": 1643,
          "aa_end": null,
          "aa_length": 1790,
          "cds_start": 4927,
          "cds_end": null,
          "cds_length": 5373,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000613657.6"
        },
        {
          "aa_ref": "S",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 35,
          "exon_rank_end": null,
          "exon_count": 35,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4906T>C",
          "hgvs_p": "p.Ser1636Pro",
          "transcript": "NM_001354411.2",
          "protein_id": "NP_001341340.1",
          "transcript_support_level": null,
          "aa_start": 1636,
          "aa_end": null,
          "aa_length": 1783,
          "cds_start": 4906,
          "cds_end": null,
          "cds_length": 5352,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001354411.2"
        },
        {
          "aa_ref": "S",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.2500T>C",
          "hgvs_p": "p.Ser834Pro",
          "transcript": "ENST00000395446.5",
          "protein_id": "ENSP00000378833.1",
          "transcript_support_level": 5,
          "aa_start": 834,
          "aa_end": null,
          "aa_length": 981,
          "cds_start": 2500,
          "cds_end": null,
          "cds_length": 2946,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000395446.5"
        },
        {
          "aa_ref": "S",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.1714T>C",
          "hgvs_p": "p.Ser572Pro",
          "transcript": "ENST00000395440.5",
          "protein_id": "ENSP00000378827.1",
          "transcript_support_level": 5,
          "aa_start": 572,
          "aa_end": null,
          "aa_length": 719,
          "cds_start": 1714,
          "cds_end": null,
          "cds_length": 2160,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000395440.5"
        },
        {
          "aa_ref": "S",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.1507T>C",
          "hgvs_p": "p.Ser503Pro",
          "transcript": "ENST00000395442.5",
          "protein_id": "ENSP00000378829.1",
          "transcript_support_level": 5,
          "aa_start": 503,
          "aa_end": null,
          "aa_length": 650,
          "cds_start": 1507,
          "cds_end": null,
          "cds_length": 1953,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000395442.5"
        },
        {
          "aa_ref": "S",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 36,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4906T>C",
          "hgvs_p": "p.Ser1636Pro",
          "transcript": "XM_047425664.1",
          "protein_id": "XP_047281620.1",
          "transcript_support_level": null,
          "aa_start": 1636,
          "aa_end": null,
          "aa_length": 1783,
          "cds_start": 4906,
          "cds_end": null,
          "cds_length": 5352,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047425664.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 36,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.*342T>C",
          "hgvs_p": null,
          "transcript": "NM_001142770.3",
          "protein_id": "NP_001136242.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1539,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 4620,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001142770.3"
        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 36,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.*342T>C",
          "hgvs_p": null,
          "transcript": "ENST00000617271.4",
          "protein_id": "ENSP00000478076.1",
          "transcript_support_level": 5,
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          "aa_length": 1539,
          "cds_start": 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": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 29,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.*342T>C",
          "hgvs_p": null,
          "transcript": "ENST00000409834.5",
          "protein_id": "ENSP00000386693.1",
          "transcript_support_level": 5,
          "aa_start": null,
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          "cds_start": null,
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          "cds_length": 3453,
          "cdna_start": null,
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        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.*414T>C",
          "hgvs_p": null,
          "transcript": "ENST00000615043.1",
          "protein_id": "ENSP00000478551.1",
          "transcript_support_level": 5,
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          "cds_start": null,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000615043.1"
        },
        {
          "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": 37,
          "intron_rank": 36,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4605+1418T>C",
          "hgvs_p": null,
          "transcript": "NM_001354429.2",
          "protein_id": "NP_001341358.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1718,
          "cds_start": null,
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          "cdna_start": null,
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          "biotype": "protein_coding",
          "feature": "NM_001354429.2"
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 36,
          "intron_rank": 35,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4497+1418T>C",
          "hgvs_p": null,
          "transcript": "NM_001142771.2",
          "protein_id": "NP_001136243.1",
          "transcript_support_level": null,
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        },
        {
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          "exon_count": 36,
          "intron_rank": 35,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4497+1418T>C",
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          "transcript": "ENST00000621708.4",
          "protein_id": "ENSP00000484454.1",
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        {
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          ],
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          "exon_count": 35,
          "intron_rank": 34,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4482+1418T>C",
          "hgvs_p": null,
          "transcript": "NM_001142772.2",
          "protein_id": "NP_001136244.1",
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          "cds_start": null,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001142772.2"
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 35,
          "intron_rank": 34,
          "intron_rank_end": null,
          "gene_symbol": "PCDH15",
          "gene_hgnc_id": 14674,
          "hgvs_c": "c.4482+1418T>C",
          "hgvs_p": null,
          "transcript": "ENST00000373965.6",
          "protein_id": "ENSP00000363076.3",
          "transcript_support_level": 5,
          "aa_start": null,
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          "aa_length": 1677,
          "cds_start": null,
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          "cds_length": 5034,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000373965.6"
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        {
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        {
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          "consequences": [
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          "transcript": "ENST00000414367.5",
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          "biotype": "nonsense_mediated_decay",
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        },
        {
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          "protein_coding": false,
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          "consequences": [
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          "biotype": "nonsense_mediated_decay",
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        },
        {
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          ],
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          "gene_symbol": "PCDH15",
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          "hgvs_c": "n.609+1418T>C",
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          "transcript": "ENST00000476074.5",
          "protein_id": null,
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          "cdna_start": null,
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          "cdna_length": null,
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          "biotype": "retained_intron",
          "feature": "ENST00000476074.5"
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      ],
      "gene_symbol": "PCDH15",
      "gene_hgnc_id": 14674,
      "dbsnp": "rs730880021",
      "frequency_reference_population": 6.841396e-7,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 1,
      "gnomad_exomes_af": 6.8414e-7,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 1,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.3679889440536499,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.288,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.4238,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 3.174,
      "phylop100way_prediction": "Benign",
      "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": 1,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,BP4",
      "acmg_by_gene": [
        {
          "score": 1,
          "benign_score": 1,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_001142769.3",
          "gene_symbol": "PCDH15",
          "hgnc_id": 14674,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.4927T>C",
          "hgvs_p": "p.Ser1643Pro"
        }
      ],
      "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
}