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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: 3-4815135-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=4815135&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 4815135,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_001378452.1",
      "consequences": [
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 59,
          "exon_rank_end": null,
          "exon_count": 62,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.7784G>A",
          "hgvs_p": "p.Gly2595Glu",
          "transcript": "NM_001378452.1",
          "protein_id": "NP_001365381.1",
          "transcript_support_level": null,
          "aa_start": 2595,
          "aa_end": null,
          "aa_length": 2758,
          "cds_start": 7784,
          "cds_end": null,
          "cds_length": 8277,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000649015.2",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001378452.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 59,
          "exon_rank_end": null,
          "exon_count": 62,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.7784G>A",
          "hgvs_p": "p.Gly2595Glu",
          "transcript": "ENST00000649015.2",
          "protein_id": "ENSP00000497605.1",
          "transcript_support_level": null,
          "aa_start": 2595,
          "aa_end": null,
          "aa_length": 2758,
          "cds_start": 7784,
          "cds_end": null,
          "cds_length": 8277,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_001378452.1",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000649015.2"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 59,
          "exon_rank_end": null,
          "exon_count": 62,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.7760G>A",
          "hgvs_p": "p.Gly2587Glu",
          "transcript": "ENST00000354582.12",
          "protein_id": "ENSP00000346595.8",
          "transcript_support_level": 5,
          "aa_start": 2587,
          "aa_end": null,
          "aa_length": 2750,
          "cds_start": 7760,
          "cds_end": null,
          "cds_length": 8253,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000354582.12"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 59,
          "exon_rank_end": null,
          "exon_count": 62,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.7757G>A",
          "hgvs_p": "p.Gly2586Glu",
          "transcript": "ENST00000648266.1",
          "protein_id": "ENSP00000498014.1",
          "transcript_support_level": null,
          "aa_start": 2586,
          "aa_end": null,
          "aa_length": 2749,
          "cds_start": 7757,
          "cds_end": null,
          "cds_length": 8250,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000648266.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 58,
          "exon_rank_end": null,
          "exon_count": 61,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.7742G>A",
          "hgvs_p": "p.Gly2581Glu",
          "transcript": "ENST00000650294.1",
          "protein_id": "ENSP00000498056.1",
          "transcript_support_level": null,
          "aa_start": 2581,
          "aa_end": null,
          "aa_length": 2744,
          "cds_start": 7742,
          "cds_end": null,
          "cds_length": 8235,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000650294.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 58,
          "exon_rank_end": null,
          "exon_count": 61,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.7739G>A",
          "hgvs_p": "p.Gly2580Glu",
          "transcript": "ENST00000443694.5",
          "protein_id": "ENSP00000401671.2",
          "transcript_support_level": 1,
          "aa_start": 2580,
          "aa_end": null,
          "aa_length": 2743,
          "cds_start": 7739,
          "cds_end": null,
          "cds_length": 8232,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000443694.5"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 56,
          "exon_rank_end": null,
          "exon_count": 59,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.7712G>A",
          "hgvs_p": "p.Gly2571Glu",
          "transcript": "ENST00000648309.1",
          "protein_id": "ENSP00000497026.1",
          "transcript_support_level": null,
          "aa_start": 2571,
          "aa_end": null,
          "aa_length": 2734,
          "cds_start": 7712,
          "cds_end": null,
          "cds_length": 8205,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000648309.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 56,
          "exon_rank_end": null,
          "exon_count": 59,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.7640G>A",
          "hgvs_p": "p.Gly2547Glu",
          "transcript": "ENST00000357086.10",
          "protein_id": "ENSP00000349597.4",
          "transcript_support_level": 1,
          "aa_start": 2547,
          "aa_end": null,
          "aa_length": 2710,
          "cds_start": 7640,
          "cds_end": null,
          "cds_length": 8133,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000357086.10"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 55,
          "exon_rank_end": null,
          "exon_count": 58,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.7595G>A",
          "hgvs_p": "p.Gly2532Glu",
          "transcript": "ENST00000456211.8",
          "protein_id": "ENSP00000397885.2",
          "transcript_support_level": 1,
          "aa_start": 2532,
          "aa_end": null,
          "aa_length": 2695,
          "cds_start": 7595,
          "cds_end": null,
          "cds_length": 8088,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000456211.8"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 39,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.5546G>A",
          "hgvs_p": "p.Gly1849Glu",
          "transcript": "ENST00000648038.1",
          "protein_id": "ENSP00000497872.1",
          "transcript_support_level": null,
          "aa_start": 1849,
          "aa_end": null,
          "aa_length": 2012,
          "cds_start": 5546,
          "cds_end": null,
          "cds_length": 6039,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000648038.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 39,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.4961G>A",
          "hgvs_p": "p.Gly1654Glu",
          "transcript": "ENST00000648431.1",
          "protein_id": "ENSP00000498149.1",
          "transcript_support_level": null,
          "aa_start": 1654,
          "aa_end": null,
          "aa_length": 1817,
          "cds_start": 4961,
          "cds_end": null,
          "cds_length": 5454,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000648431.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 39,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.4724G>A",
          "hgvs_p": "p.Gly1575Glu",
          "transcript": "ENST00000648212.1",
          "protein_id": "ENSP00000498022.1",
          "transcript_support_level": null,
          "aa_start": 1575,
          "aa_end": null,
          "aa_length": 1738,
          "cds_start": 4724,
          "cds_end": null,
          "cds_length": 5217,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000648212.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.1673G>A",
          "hgvs_p": "p.Gly558Glu",
          "transcript": "ENST00000544951.6",
          "protein_id": "ENSP00000440564.1",
          "transcript_support_level": 1,
          "aa_start": 558,
          "aa_end": null,
          "aa_length": 721,
          "cds_start": 1673,
          "cds_end": null,
          "cds_length": 2166,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000544951.6"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 58,
          "exon_rank_end": null,
          "exon_count": 61,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.7739G>A",
          "hgvs_p": "p.Gly2580Glu",
          "transcript": "NM_001168272.2",
          "protein_id": "NP_001161744.1",
          "transcript_support_level": null,
          "aa_start": 2580,
          "aa_end": null,
          "aa_length": 2743,
          "cds_start": 7739,
          "cds_end": null,
          "cds_length": 8232,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001168272.2"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 56,
          "exon_rank_end": null,
          "exon_count": 59,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.7640G>A",
          "hgvs_p": "p.Gly2547Glu",
          "transcript": "NM_001099952.4",
          "protein_id": "NP_001093422.2",
          "transcript_support_level": null,
          "aa_start": 2547,
          "aa_end": null,
          "aa_length": 2710,
          "cds_start": 7640,
          "cds_end": null,
          "cds_length": 8133,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001099952.4"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 55,
          "exon_rank_end": null,
          "exon_count": 58,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.7595G>A",
          "hgvs_p": "p.Gly2532Glu",
          "transcript": "NM_002222.7",
          "protein_id": "NP_002213.5",
          "transcript_support_level": null,
          "aa_start": 2532,
          "aa_end": null,
          "aa_length": 2695,
          "cds_start": 7595,
          "cds_end": null,
          "cds_length": 8088,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_002222.7"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 31,
          "exon_rank_end": null,
          "exon_count": 34,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.4151G>A",
          "hgvs_p": "p.Gly1384Glu",
          "transcript": "ENST00000648016.1",
          "protein_id": "ENSP00000496893.1",
          "transcript_support_level": null,
          "aa_start": 1384,
          "aa_end": null,
          "aa_length": 1547,
          "cds_start": 4151,
          "cds_end": null,
          "cds_length": 4644,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000648016.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.116G>A",
          "hgvs_p": "p.Gly39Glu",
          "transcript": "ENST00000478515.2",
          "protein_id": "ENSP00000497999.1",
          "transcript_support_level": 3,
          "aa_start": 39,
          "aa_end": null,
          "aa_length": 186,
          "cds_start": 116,
          "cds_end": null,
          "cds_length": 563,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000478515.2"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.35G>A",
          "hgvs_p": "p.Gly12Glu",
          "transcript": "ENST00000647685.1",
          "protein_id": "ENSP00000497835.1",
          "transcript_support_level": null,
          "aa_start": 12,
          "aa_end": null,
          "aa_length": 175,
          "cds_start": 35,
          "cds_end": null,
          "cds_length": 528,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000647685.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "E",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ITPR1",
          "gene_hgnc_id": 6180,
          "hgvs_c": "c.35G>A",
          "hgvs_p": "p.Gly12Glu",
          "transcript": "ENST00000649139.1",
          "protein_id": "ENSP00000497226.1",
          "transcript_support_level": null,
          "aa_start": 12,
          "aa_end": null,
          "aa_length": 175,
          "cds_start": 35,
          "cds_end": null,
          "cds_length": 528,
          "cdna_start": null,
          "cdna_end": null,
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      "gene_symbol": "ITPR1",
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      "dbsnp": "rs869312685",
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      "hom_count_reference_population": 0,
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      "gnomad_exomes_af": null,
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      "gnomad_mito_homoplasmic": null,
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      "computational_score_selected": 0.9359696507453918,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.44999998807907104,
      "splice_prediction_selected": "Uncertain_significance",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.957,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9998,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.6,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 9.92,
      "phylop100way_prediction": "Pathogenic",
      "spliceai_max_score": 0.45,
      "spliceai_max_prediction": "Uncertain_significance",
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
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      "acmg_score": 16,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PM1,PM2,PM5,PP3_Moderate,PP5_Very_Strong",
      "acmg_by_gene": [
        {
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          "criteria": [
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            "PM2",
            "PM5",
            "PP3_Moderate",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "NM_001378452.1",
          "gene_symbol": "ITPR1",
          "hgnc_id": 6180,
          "effects": [
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          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.7784G>A",
          "hgvs_p": "p.Gly2595Glu"
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        {
          "score": 12,
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          "pathogenic_score": 12,
          "criteria": [
            "PM2",
            "PP3_Moderate",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000474544.4",
          "gene_symbol": "ENSG00000235978",
          "hgnc_id": null,
          "effects": [
            "non_coding_transcript_exon_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.39C>T",
          "hgvs_p": null
        },
        {
          "score": 12,
          "benign_score": 0,
          "pathogenic_score": 12,
          "criteria": [
            "PM2",
            "PP3_Moderate",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "XR_007095790.1",
          "gene_symbol": "LOC124906209",
          "hgnc_id": null,
          "effects": [
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          ],
          "inheritance_mode": "",
          "hgvs_c": "n.274-704C>T",
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        }
      ],
      "clinvar_disease": "Spinocerebellar ataxia type 15/16,not provided",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "P:3",
      "phenotype_combined": "Spinocerebellar ataxia type 15/16|not provided",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}