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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: 2-24793223-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=24793223&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "2",
      "pos": 24793223,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "NM_001013663.2",
      "consequences": [
        {
          "aa_ref": "C",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTRHD1",
          "gene_hgnc_id": 33782,
          "hgvs_c": "c.155G>A",
          "hgvs_p": "p.Cys52Tyr",
          "transcript": "NM_001013663.2",
          "protein_id": "NP_001013685.1",
          "transcript_support_level": null,
          "aa_start": 52,
          "aa_end": null,
          "aa_length": 140,
          "cds_start": 155,
          "cds_end": null,
          "cds_length": 423,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000328379.6",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001013663.2"
        },
        {
          "aa_ref": "C",
          "aa_alt": "Y",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTRHD1",
          "gene_hgnc_id": 33782,
          "hgvs_c": "c.155G>A",
          "hgvs_p": "p.Cys52Tyr",
          "transcript": "ENST00000328379.6",
          "protein_id": "ENSP00000330389.4",
          "transcript_support_level": 1,
          "aa_start": 52,
          "aa_end": null,
          "aa_length": 140,
          "cds_start": 155,
          "cds_end": null,
          "cds_length": 423,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_001013663.2",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000328379.6"
        },
        {
          "aa_ref": "C",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTRHD1",
          "gene_hgnc_id": 33782,
          "hgvs_c": "c.155G>A",
          "hgvs_p": "p.Cys52Tyr",
          "transcript": "ENST00000915622.1",
          "protein_id": "ENSP00000585681.1",
          "transcript_support_level": null,
          "aa_start": 52,
          "aa_end": null,
          "aa_length": 137,
          "cds_start": 155,
          "cds_end": null,
          "cds_length": 414,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000915622.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "5_prime_UTR_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "c.-347C>T",
          "hgvs_p": null,
          "transcript": "ENST00000868050.1",
          "protein_id": "ENSP00000538109.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 300,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 903,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000868050.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "5_prime_UTR_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "c.-251C>T",
          "hgvs_p": null,
          "transcript": "ENST00000473706.5",
          "protein_id": "ENSP00000417787.1",
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 294,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 885,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000473706.5"
        },
        {
          "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": 8,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "c.-615+59C>T",
          "hgvs_p": null,
          "transcript": "ENST00000868051.1",
          "protein_id": "ENSP00000538110.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 300,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 903,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000868051.1"
        },
        {
          "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": 2,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PTRHD1",
          "gene_hgnc_id": 33782,
          "hgvs_c": "c.69+86G>A",
          "hgvs_p": null,
          "transcript": "ENST00000915621.1",
          "protein_id": "ENSP00000585680.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 79,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 240,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000915621.1"
        },
        {
          "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": 4,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "n.29+59C>T",
          "hgvs_p": null,
          "transcript": "ENST00000473476.5",
          "protein_id": null,
          "transcript_support_level": 4,
          "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": "ENST00000473476.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "c.-347C>T",
          "hgvs_p": null,
          "transcript": "NM_001322101.2",
          "protein_id": "NP_001309030.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 300,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 903,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000380834.7",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001322101.2"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "c.-347C>T",
          "hgvs_p": null,
          "transcript": "ENST00000380834.7",
          "protein_id": "ENSP00000370214.2",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 300,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 903,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_001322101.2",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000380834.7"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "c.-366C>T",
          "hgvs_p": null,
          "transcript": "ENST00000260662.2",
          "protein_id": "ENSP00000260662.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 300,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 903,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000260662.2"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "c.-366C>T",
          "hgvs_p": null,
          "transcript": "NM_024322.4",
          "protein_id": "NP_077298.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 300,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 903,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_024322.4"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "c.-366C>T",
          "hgvs_p": null,
          "transcript": "ENST00000912477.1",
          "protein_id": "ENSP00000582536.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 300,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 903,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000912477.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "c.-366C>T",
          "hgvs_p": null,
          "transcript": "ENST00000912479.1",
          "protein_id": "ENSP00000582538.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 300,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 903,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000912479.1"
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "c.-251C>T",
          "hgvs_p": null,
          "transcript": "NM_001199803.3",
          "protein_id": "NP_001186732.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 294,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 885,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001199803.3"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTRHD1",
          "gene_hgnc_id": 33782,
          "hgvs_c": "n.-149G>A",
          "hgvs_p": null,
          "transcript": "ENST00000474668.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "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": "ENST00000474668.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTRHD1",
          "gene_hgnc_id": 33782,
          "hgvs_c": "n.-170G>A",
          "hgvs_p": null,
          "transcript": "ENST00000480190.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "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": "ENST00000480190.1"
        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "n.-222C>T",
          "hgvs_p": null,
          "transcript": "ENST00000486527.6",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": 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": "retained_intron",
          "feature": "ENST00000486527.6"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTRHD1",
          "gene_hgnc_id": 33782,
          "hgvs_c": "n.-133G>A",
          "hgvs_p": null,
          "transcript": "ENST00000487316.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "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": "ENST00000487316.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CENPO",
          "gene_hgnc_id": 28152,
          "hgvs_c": "n.-177C>T",
          "hgvs_p": null,
          "transcript": "ENST00000491031.5",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000491031.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
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          "gene_symbol": "LOC105369164",
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        {
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          "transcript": "XR_939843.4",
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          "biotype": "pseudogene",
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      ],
      "gene_symbol": "PTRHD1",
      "gene_hgnc_id": 33782,
      "dbsnp": "rs781442277",
      "frequency_reference_population": 0.000001368856,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 2,
      "gnomad_exomes_af": 0.00000136886,
      "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": 0.9322865009307861,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.473,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.9734,
      "alphamissense_prediction": "Pathogenic",
      "bayesdelnoaf_score": 0.13,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 6.942,
      "phylop100way_prediction": "Uncertain_significance",
      "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,
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      "acmg_score": 6,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PM2,PP3_Moderate,PP5_Moderate",
      "acmg_by_gene": [
        {
          "score": 6,
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          "pathogenic_score": 6,
          "criteria": [
            "PM2",
            "PP3_Moderate",
            "PP5_Moderate"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "NM_001013663.2",
          "gene_symbol": "PTRHD1",
          "hgnc_id": 33782,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.155G>A",
          "hgvs_p": "p.Cys52Tyr"
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        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PM2",
            "PP3_Moderate",
            "PP5_Moderate"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000473706.5",
          "gene_symbol": "CENPO",
          "hgnc_id": 28152,
          "effects": [
            "5_prime_UTR_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.-251C>T",
          "hgvs_p": null
        },
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PM2",
            "PP3_Moderate",
            "PP5_Moderate"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "XR_939843.4",
          "gene_symbol": "LOC105369164",
          "hgnc_id": null,
          "effects": [
            "upstream_gene_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.-148G>A",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "Neurodevelopmental disorder with early-onset parkinsonism and behavioral abnormalities,Parkinsonian disorder",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "P:1",
      "phenotype_combined": "Parkinsonian disorder|Neurodevelopmental disorder with early-onset parkinsonism and behavioral abnormalities",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}