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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: 17-4967789-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=4967789&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "17",
      "pos": 4967789,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "NM_004890.3",
      "consequences": [
        {
          "aa_ref": "G",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG7",
          "gene_hgnc_id": 11216,
          "hgvs_c": "c.16G>A",
          "hgvs_p": "p.Gly6Ser",
          "transcript": "NM_004890.3",
          "protein_id": "NP_004881.2",
          "transcript_support_level": null,
          "aa_start": 6,
          "aa_end": null,
          "aa_length": 227,
          "cds_start": 16,
          "cds_end": null,
          "cds_length": 684,
          "cdna_start": 29,
          "cdna_end": null,
          "cdna_length": 1005,
          "mane_select": "ENST00000206020.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "G",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG7",
          "gene_hgnc_id": 11216,
          "hgvs_c": "c.16G>A",
          "hgvs_p": "p.Gly6Ser",
          "transcript": "ENST00000206020.8",
          "protein_id": "ENSP00000206020.3",
          "transcript_support_level": 1,
          "aa_start": 6,
          "aa_end": null,
          "aa_length": 227,
          "cds_start": 16,
          "cds_end": null,
          "cds_length": 684,
          "cdna_start": 29,
          "cdna_end": null,
          "cdna_length": 1005,
          "mane_select": "NM_004890.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "5_prime_UTR_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG7",
          "gene_hgnc_id": 11216,
          "hgvs_c": "c.-18G>A",
          "hgvs_p": null,
          "transcript": "ENST00000575142.5",
          "protein_id": "ENSP00000461145.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 194,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 585,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1094,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG7",
          "gene_hgnc_id": 11216,
          "hgvs_c": "n.20G>A",
          "hgvs_p": null,
          "transcript": "ENST00000571023.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 579,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG7",
          "gene_hgnc_id": 11216,
          "hgvs_c": "n.-18G>A",
          "hgvs_p": null,
          "transcript": "ENST00000575784.2",
          "protein_id": "ENSP00000458264.1",
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 694,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "5_prime_UTR_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG7",
          "gene_hgnc_id": 11216,
          "hgvs_c": "n.-18G>A",
          "hgvs_p": null,
          "transcript": "ENST00000575784.2",
          "protein_id": "ENSP00000458264.1",
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 694,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CAMTA2",
          "gene_hgnc_id": 18807,
          "hgvs_c": "c.*967G>A",
          "hgvs_p": null,
          "transcript": "NM_015099.4",
          "protein_id": "NP_055914.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1202,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3609,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4515,
          "mane_select": "ENST00000348066.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CAMTA2",
          "gene_hgnc_id": 18807,
          "hgvs_c": "c.*967G>A",
          "hgvs_p": null,
          "transcript": "ENST00000348066.8",
          "protein_id": "ENSP00000321813.7",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1202,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3609,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4515,
          "mane_select": "NM_015099.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CAMTA2",
          "gene_hgnc_id": 18807,
          "hgvs_c": "c.*917G>A",
          "hgvs_p": null,
          "transcript": "ENST00000414043.7",
          "protein_id": "ENSP00000412886.3",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1241,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3726,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4589,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CAMTA2",
          "gene_hgnc_id": 18807,
          "hgvs_c": "c.*967G>A",
          "hgvs_p": null,
          "transcript": "ENST00000361571.9",
          "protein_id": "ENSP00000354828.5",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1201,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3606,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4777,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CAMTA2",
          "gene_hgnc_id": 18807,
          "hgvs_c": "c.*967G>A",
          "hgvs_p": null,
          "transcript": "ENST00000381311.9",
          "protein_id": "ENSP00000370712.5",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1197,
          "cds_start": -4,
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          "cds_length": 3594,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4374,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "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": "SPAG7",
          "gene_hgnc_id": 11216,
          "hgvs_c": "n.-4G>A",
          "hgvs_p": null,
          "transcript": "ENST00000573805.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
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          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000262429",
          "gene_hgnc_id": null,
          "hgvs_c": "n.-206C>T",
          "hgvs_p": null,
          "transcript": "ENST00000576752.1",
          "protein_id": null,
          "transcript_support_level": 5,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
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          "mane_select": null,
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          "feature": null
        },
        {
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          "canonical": false,
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          "strand": true,
          "consequences": [
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          ],
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          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LOC124900387",
          "gene_hgnc_id": null,
          "hgvs_c": "n.-76G>A",
          "hgvs_p": null,
          "transcript": "XR_007065587.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 1811,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
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          "gene_symbol": "CAMTA2",
          "gene_hgnc_id": 18807,
          "hgvs_c": "c.*917G>A",
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          "transcript": "NM_001171167.2",
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        {
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          "canonical": false,
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          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
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          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CAMTA2",
          "gene_hgnc_id": 18807,
          "hgvs_c": "c.*967G>A",
          "hgvs_p": null,
          "transcript": "ENST00000572543.5",
          "protein_id": "ENSP00000460779.1",
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          "aa_start": null,
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          "cds_length": 3624,
          "cdna_start": null,
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          "cdna_length": 4496,
          "mane_select": null,
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          "biotype": null,
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        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
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          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CAMTA2",
          "gene_hgnc_id": 18807,
          "hgvs_c": "c.*967G>A",
          "hgvs_p": null,
          "transcript": "NM_001171168.2",
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        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
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          "exon_count": 21,
          "intron_rank": null,
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          "gene_symbol": "CAMTA2",
          "gene_hgnc_id": 18807,
          "hgvs_c": "c.*967G>A",
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          "transcript": "NM_001171166.2",
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        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "CAMTA2",
          "gene_hgnc_id": 18807,
          "hgvs_c": "n.*4136G>A",
          "hgvs_p": null,
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        {
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
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          "exon_count": 23,
          "intron_rank": null,
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          "gene_symbol": "CAMTA2",
          "gene_hgnc_id": 18807,
          "hgvs_c": "c.*967G>A",
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          "transcript": "XM_011523746.4",
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          "cds_length": 3693,
          "cdna_start": null,
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          "cdna_length": 4955,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
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          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CAMTA2",
          "gene_hgnc_id": 18807,
          "hgvs_c": "c.*967G>A",
          "hgvs_p": null,
          "transcript": "XM_011523747.4",
          "protein_id": "XP_011522049.1",
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          "aa_length": 1225,
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        }
      ],
      "gene_symbol": "SPAG7",
      "gene_hgnc_id": 11216,
      "dbsnp": null,
      "frequency_reference_population": null,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 0,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.7640895843505859,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.341,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.5268,
      "alphamissense_prediction": "Uncertain_significance",
      "bayesdelnoaf_score": -0.09,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 5.974,
      "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,
      "mitotip_prediction": null,
      "acmg_score": 3,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,PP3",
      "acmg_by_gene": [
        {
          "score": 3,
          "benign_score": 0,
          "pathogenic_score": 3,
          "criteria": [
            "PM2",
            "PP3"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_004890.3",
          "gene_symbol": "SPAG7",
          "hgnc_id": 11216,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.16G>A",
          "hgvs_p": "p.Gly6Ser"
        },
        {
          "score": 3,
          "benign_score": 0,
          "pathogenic_score": 3,
          "criteria": [
            "PM2",
            "PP3"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_015099.4",
          "gene_symbol": "CAMTA2",
          "hgnc_id": 18807,
          "effects": [
            "downstream_gene_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.*967G>A",
          "hgvs_p": null
        },
        {
          "score": 3,
          "benign_score": 0,
          "pathogenic_score": 3,
          "criteria": [
            "PM2",
            "PP3"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "XR_007065587.1",
          "gene_symbol": "LOC124900387",
          "hgnc_id": null,
          "effects": [
            "upstream_gene_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.-76G>A",
          "hgvs_p": null
        },
        {
          "score": 3,
          "benign_score": 0,
          "pathogenic_score": 3,
          "criteria": [
            "PM2",
            "PP3"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000576752.1",
          "gene_symbol": "ENSG00000262429",
          "hgnc_id": null,
          "effects": [
            "upstream_gene_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.-206C>T",
          "hgvs_p": null
        }
      ],
      "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
}