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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: 4-107950250-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=107950250&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "4",
      "pos": 107950250,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "NM_183075.3",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1",
          "gene_hgnc_id": 20582,
          "hgvs_c": "c.1462C>T",
          "hgvs_p": "p.Arg488Trp",
          "transcript": "NM_183075.3",
          "protein_id": "NP_898898.1",
          "transcript_support_level": null,
          "aa_start": 488,
          "aa_end": null,
          "aa_length": 544,
          "cds_start": 1462,
          "cds_end": null,
          "cds_length": 1635,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000332884.11",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_183075.3"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1",
          "gene_hgnc_id": 20582,
          "hgvs_c": "c.1462C>T",
          "hgvs_p": "p.Arg488Trp",
          "transcript": "ENST00000332884.11",
          "protein_id": "ENSP00000333212.6",
          "transcript_support_level": 1,
          "aa_start": 488,
          "aa_end": null,
          "aa_length": 544,
          "cds_start": 1462,
          "cds_end": null,
          "cds_length": 1635,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_183075.3",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000332884.11"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1",
          "gene_hgnc_id": 20582,
          "hgvs_c": "c.835C>T",
          "hgvs_p": "p.Arg279Trp",
          "transcript": "ENST00000508453.1",
          "protein_id": "ENSP00000423667.1",
          "transcript_support_level": 1,
          "aa_start": 279,
          "aa_end": null,
          "aa_length": 335,
          "cds_start": 835,
          "cds_end": null,
          "cds_length": 1008,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000508453.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1",
          "gene_hgnc_id": 20582,
          "hgvs_c": "c.1072C>T",
          "hgvs_p": "p.Arg358Trp",
          "transcript": "ENST00000908818.1",
          "protein_id": "ENSP00000578877.1",
          "transcript_support_level": null,
          "aa_start": 358,
          "aa_end": null,
          "aa_length": 414,
          "cds_start": 1072,
          "cds_end": null,
          "cds_length": 1245,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000908818.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "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": "CYP2U1",
          "gene_hgnc_id": 20582,
          "hgvs_c": "c.880C>T",
          "hgvs_p": "p.Arg294Trp",
          "transcript": "ENST00000917361.1",
          "protein_id": "ENSP00000587420.1",
          "transcript_support_level": null,
          "aa_start": 294,
          "aa_end": null,
          "aa_length": 350,
          "cds_start": 880,
          "cds_end": null,
          "cds_length": 1053,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000917361.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "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": "CYP2U1",
          "gene_hgnc_id": 20582,
          "hgvs_c": "c.826C>T",
          "hgvs_p": "p.Arg276Trp",
          "transcript": "ENST00000908819.1",
          "protein_id": "ENSP00000578878.1",
          "transcript_support_level": null,
          "aa_start": 276,
          "aa_end": null,
          "aa_length": 332,
          "cds_start": 826,
          "cds_end": null,
          "cds_length": 999,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000908819.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1",
          "gene_hgnc_id": 20582,
          "hgvs_c": "c.664C>T",
          "hgvs_p": "p.Arg222Trp",
          "transcript": "ENST00000908820.1",
          "protein_id": "ENSP00000578879.1",
          "transcript_support_level": null,
          "aa_start": 222,
          "aa_end": null,
          "aa_length": 278,
          "cds_start": 664,
          "cds_end": null,
          "cds_length": 837,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000908820.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1",
          "gene_hgnc_id": 20582,
          "hgvs_c": "c.1516C>T",
          "hgvs_p": "p.Arg506Trp",
          "transcript": "XM_005262717.2",
          "protein_id": "XP_005262774.1",
          "transcript_support_level": null,
          "aa_start": 506,
          "aa_end": null,
          "aa_length": 562,
          "cds_start": 1516,
          "cds_end": null,
          "cds_length": 1689,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_005262717.2"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "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": "CYP2U1",
          "gene_hgnc_id": 20582,
          "hgvs_c": "c.826C>T",
          "hgvs_p": "p.Arg276Trp",
          "transcript": "XM_005262720.2",
          "protein_id": "XP_005262777.1",
          "transcript_support_level": null,
          "aa_start": 276,
          "aa_end": null,
          "aa_length": 332,
          "cds_start": 826,
          "cds_end": null,
          "cds_length": 999,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_005262720.2"
        },
        {
          "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": "CYP2U1-AS1",
          "gene_hgnc_id": 54817,
          "hgvs_c": "n.263+28470G>A",
          "hgvs_p": null,
          "transcript": "ENST00000513071.2",
          "protein_id": null,
          "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": "pseudogene",
          "feature": "ENST00000513071.2"
        },
        {
          "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": 10,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1-AS1",
          "gene_hgnc_id": 54817,
          "hgvs_c": "n.80+28470G>A",
          "hgvs_p": null,
          "transcript": "ENST00000656249.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": "ENST00000656249.1"
        },
        {
          "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": "CYP2U1-AS1",
          "gene_hgnc_id": 54817,
          "hgvs_c": "n.194+39318G>A",
          "hgvs_p": null,
          "transcript": "ENST00000658105.4",
          "protein_id": null,
          "transcript_support_level": null,
          "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": "ENST00000658105.4"
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1-AS1",
          "gene_hgnc_id": 54817,
          "hgvs_c": "n.129-28240G>A",
          "hgvs_p": null,
          "transcript": "ENST00000686573.3",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000686573.3"
        },
        {
          "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": 4,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1-AS1",
          "gene_hgnc_id": 54817,
          "hgvs_c": "n.131+39318G>A",
          "hgvs_p": null,
          "transcript": "ENST00000687236.2",
          "protein_id": null,
          "transcript_support_level": null,
          "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": "ENST00000687236.2"
        },
        {
          "aa_ref": null,
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          "canonical": false,
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          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1-AS1",
          "gene_hgnc_id": 54817,
          "hgvs_c": "n.132-28240G>A",
          "hgvs_p": null,
          "transcript": "ENST00000702404.2",
          "protein_id": null,
          "transcript_support_level": null,
          "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": "ENST00000702404.2"
        },
        {
          "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": 4,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1-AS1",
          "gene_hgnc_id": 54817,
          "hgvs_c": "n.126-28240G>A",
          "hgvs_p": null,
          "transcript": "ENST00000781789.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": "ENST00000781789.1"
        },
        {
          "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": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1-AS1",
          "gene_hgnc_id": 54817,
          "hgvs_c": "n.125+39318G>A",
          "hgvs_p": null,
          "transcript": "ENST00000781790.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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,
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          "biotype": "pseudogene",
          "feature": "ENST00000781790.1"
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1-AS1",
          "gene_hgnc_id": 54817,
          "hgvs_c": "n.126-28240G>A",
          "hgvs_p": null,
          "transcript": "ENST00000781791.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "aa_length": null,
          "cds_start": null,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000781791.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 5,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1-AS1",
          "gene_hgnc_id": 54817,
          "hgvs_c": "n.126-28240G>A",
          "hgvs_p": null,
          "transcript": "ENST00000781792.1",
          "protein_id": null,
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          "aa_start": null,
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          "cds_start": null,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000781792.1"
        },
        {
          "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": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CYP2U1-AS1",
          "gene_hgnc_id": 54817,
          "hgvs_c": "n.158-12859G>A",
          "hgvs_p": null,
          "transcript": "ENST00000781793.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": "ENST00000781793.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
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          "exon_count": 2,
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          "gene_symbol": "LOC107986298",
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        {
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          "consequences": [
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          "gene_symbol": "CYP2U1-AS1",
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          "hgvs_c": "n.*125G>A",
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          "transcript": "ENST00000781797.1",
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          "biotype": "pseudogene",
          "feature": "ENST00000781797.1"
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      ],
      "gene_symbol": "CYP2U1",
      "gene_hgnc_id": 20582,
      "dbsnp": "rs141431913",
      "frequency_reference_population": 0.00007398351,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 118,
      "gnomad_exomes_af": 0.000077612,
      "gnomad_genomes_af": 0.0000395064,
      "gnomad_exomes_ac": 112,
      "gnomad_genomes_ac": 6,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.9627587795257568,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.05000000074505806,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.939,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9388,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.46,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 3.057,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.05,
      "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": 16,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PM2,PM5,PP3_Strong,PP5_Very_Strong",
      "acmg_by_gene": [
        {
          "score": 16,
          "benign_score": 0,
          "pathogenic_score": 16,
          "criteria": [
            "PM2",
            "PM5",
            "PP3_Strong",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "NM_183075.3",
          "gene_symbol": "CYP2U1",
          "hgnc_id": 20582,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1462C>T",
          "hgvs_p": "p.Arg488Trp"
        },
        {
          "score": 14,
          "benign_score": 0,
          "pathogenic_score": 14,
          "criteria": [
            "PM2",
            "PP3_Strong",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000513071.2",
          "gene_symbol": "CYP2U1-AS1",
          "hgnc_id": 54817,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.263+28470G>A",
          "hgvs_p": null
        },
        {
          "score": 14,
          "benign_score": 0,
          "pathogenic_score": 14,
          "criteria": [
            "PM2",
            "PP3_Strong",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "XR_001741784.2",
          "gene_symbol": "LOC107986298",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.204+28470G>A",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "Hereditary spastic paraplegia,Hereditary spastic paraplegia 56,Spastic paraplegia,not provided",
      "clinvar_classification": "Pathogenic/Likely pathogenic",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "P:3 LP:2",
      "phenotype_combined": "Hereditary spastic paraplegia 56|Spastic paraplegia|Hereditary spastic paraplegia|not provided",
      "pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}