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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: 1-147187081-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=147187081&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 147187081,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "NM_001461.4",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1421G>A",
          "hgvs_p": "p.Arg474His",
          "transcript": "NM_001461.4",
          "protein_id": "NP_001452.2",
          "transcript_support_level": null,
          "aa_start": 474,
          "aa_end": null,
          "aa_length": 533,
          "cds_start": 1421,
          "cds_end": null,
          "cds_length": 1602,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000254090.9",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001461.4"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1421G>A",
          "hgvs_p": "p.Arg474His",
          "transcript": "ENST00000254090.9",
          "protein_id": "ENSP00000254090.4",
          "transcript_support_level": 1,
          "aa_start": 474,
          "aa_end": null,
          "aa_length": 533,
          "cds_start": 1421,
          "cds_end": null,
          "cds_length": 1602,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_001461.4",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000254090.9"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.*210G>A",
          "hgvs_p": null,
          "transcript": "ENST00000369272.7",
          "protein_id": "ENSP00000358277.3",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 285,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 858,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000369272.7"
        },
        {
          "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": 9,
          "intron_rank": 8,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1257-2451G>A",
          "hgvs_p": null,
          "transcript": "ENST00000441068.6",
          "protein_id": "ENSP00000416011.2",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 464,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1395,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000441068.6"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1433G>A",
          "hgvs_p": "p.Arg478His",
          "transcript": "ENST00000865850.1",
          "protein_id": "ENSP00000535909.1",
          "transcript_support_level": null,
          "aa_start": 478,
          "aa_end": null,
          "aa_length": 537,
          "cds_start": 1433,
          "cds_end": null,
          "cds_length": 1614,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000865850.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1433G>A",
          "hgvs_p": "p.Arg478His",
          "transcript": "ENST00000865857.1",
          "protein_id": "ENSP00000535916.1",
          "transcript_support_level": null,
          "aa_start": 478,
          "aa_end": null,
          "aa_length": 537,
          "cds_start": 1433,
          "cds_end": null,
          "cds_length": 1614,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000865857.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1433G>A",
          "hgvs_p": "p.Arg478His",
          "transcript": "ENST00000865858.1",
          "protein_id": "ENSP00000535917.1",
          "transcript_support_level": null,
          "aa_start": 478,
          "aa_end": null,
          "aa_length": 537,
          "cds_start": 1433,
          "cds_end": null,
          "cds_length": 1614,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000865858.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1433G>A",
          "hgvs_p": "p.Arg478His",
          "transcript": "ENST00000942493.1",
          "protein_id": "ENSP00000612552.1",
          "transcript_support_level": null,
          "aa_start": 478,
          "aa_end": null,
          "aa_length": 537,
          "cds_start": 1433,
          "cds_end": null,
          "cds_length": 1614,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000942493.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1433G>A",
          "hgvs_p": "p.Arg478His",
          "transcript": "ENST00000942494.1",
          "protein_id": "ENSP00000612553.1",
          "transcript_support_level": null,
          "aa_start": 478,
          "aa_end": null,
          "aa_length": 537,
          "cds_start": 1433,
          "cds_end": null,
          "cds_length": 1614,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000942494.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1421G>A",
          "hgvs_p": "p.Arg474His",
          "transcript": "ENST00000865847.1",
          "protein_id": "ENSP00000535906.1",
          "transcript_support_level": null,
          "aa_start": 474,
          "aa_end": null,
          "aa_length": 533,
          "cds_start": 1421,
          "cds_end": null,
          "cds_length": 1602,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000865847.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1421G>A",
          "hgvs_p": "p.Arg474His",
          "transcript": "ENST00000865848.1",
          "protein_id": "ENSP00000535907.1",
          "transcript_support_level": null,
          "aa_start": 474,
          "aa_end": null,
          "aa_length": 533,
          "cds_start": 1421,
          "cds_end": null,
          "cds_length": 1602,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000865848.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1421G>A",
          "hgvs_p": "p.Arg474His",
          "transcript": "ENST00000865849.1",
          "protein_id": "ENSP00000535908.1",
          "transcript_support_level": null,
          "aa_start": 474,
          "aa_end": null,
          "aa_length": 533,
          "cds_start": 1421,
          "cds_end": null,
          "cds_length": 1602,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000865849.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1421G>A",
          "hgvs_p": "p.Arg474His",
          "transcript": "ENST00000865851.1",
          "protein_id": "ENSP00000535910.1",
          "transcript_support_level": null,
          "aa_start": 474,
          "aa_end": null,
          "aa_length": 533,
          "cds_start": 1421,
          "cds_end": null,
          "cds_length": 1602,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000865851.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1421G>A",
          "hgvs_p": "p.Arg474His",
          "transcript": "ENST00000865855.1",
          "protein_id": "ENSP00000535914.1",
          "transcript_support_level": null,
          "aa_start": 474,
          "aa_end": null,
          "aa_length": 533,
          "cds_start": 1421,
          "cds_end": null,
          "cds_length": 1602,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000865855.1"
        },
        {
          "aa_ref": "R",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1421G>A",
          "hgvs_p": "p.Arg474His",
          "transcript": "ENST00000865859.1",
          "protein_id": "ENSP00000535918.1",
          "transcript_support_level": null,
          "aa_start": 474,
          "aa_end": null,
          "aa_length": 533,
          "cds_start": 1421,
          "cds_end": null,
          "cds_length": 1602,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000865859.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1421G>A",
          "hgvs_p": "p.Arg474His",
          "transcript": "ENST00000865864.1",
          "protein_id": "ENSP00000535923.1",
          "transcript_support_level": null,
          "aa_start": 474,
          "aa_end": null,
          "aa_length": 533,
          "cds_start": 1421,
          "cds_end": null,
          "cds_length": 1602,
          "cdna_start": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000865864.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1421G>A",
          "hgvs_p": "p.Arg474His",
          "transcript": "ENST00000865866.1",
          "protein_id": "ENSP00000535925.1",
          "transcript_support_level": null,
          "aa_start": 474,
          "aa_end": null,
          "aa_length": 533,
          "cds_start": 1421,
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          "cdna_start": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "R",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
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          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1421G>A",
          "hgvs_p": "p.Arg474His",
          "transcript": "ENST00000865868.1",
          "protein_id": "ENSP00000535927.1",
          "transcript_support_level": null,
          "aa_start": 474,
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          "aa_length": 533,
          "cds_start": 1421,
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          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000865868.1"
        },
        {
          "aa_ref": "R",
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          "protein_coding": true,
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          "consequences": [
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          ],
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          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1358G>A",
          "hgvs_p": "p.Arg453His",
          "transcript": "ENST00000865854.1",
          "protein_id": "ENSP00000535913.1",
          "transcript_support_level": null,
          "aa_start": 453,
          "aa_end": null,
          "aa_length": 512,
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          "cds_length": 1539,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000865854.1"
        },
        {
          "aa_ref": "R",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO5",
          "gene_hgnc_id": 3773,
          "hgvs_c": "c.1358G>A",
          "hgvs_p": "p.Arg453His",
          "transcript": "ENST00000865869.1",
          "protein_id": "ENSP00000535928.1",
          "transcript_support_level": null,
          "aa_start": 453,
          "aa_end": null,
          "aa_length": 512,
          "cds_start": 1358,
          "cds_end": null,
          "cds_length": 1539,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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      ],
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      "gene_hgnc_id": 3773,
      "dbsnp": "rs374261975",
      "frequency_reference_population": 0.00006133601,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 99,
      "gnomad_exomes_af": 0.0000629327,
      "gnomad_genomes_af": 0.0000459976,
      "gnomad_exomes_ac": 92,
      "gnomad_genomes_ac": 7,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.40533870458602905,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.733,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.6948,
      "alphamissense_prediction": "Pathogenic",
      "bayesdelnoaf_score": 0.26,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 5.951,
      "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": -4,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "PP3,BP4,BS2",
      "acmg_by_gene": [
        {
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          "benign_score": 5,
          "pathogenic_score": 1,
          "criteria": [
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            "BP4",
            "BS2"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_001461.4",
          "gene_symbol": "FMO5",
          "hgnc_id": 3773,
          "effects": [
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          "inheritance_mode": "AD",
          "hgvs_c": "c.1421G>A",
          "hgvs_p": "p.Arg474His"
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        {
          "score": -4,
          "benign_score": 5,
          "pathogenic_score": 1,
          "criteria": [
            "PP3",
            "BP4",
            "BS2"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_001348451.2",
          "gene_symbol": "CHD1L",
          "hgnc_id": 1916,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.-90+12496C>T",
          "hgvs_p": null
        },
        {
          "score": 0,
          "benign_score": 1,
          "pathogenic_score": 1,
          "criteria": [
            "PP3",
            "BP4"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000606757.1",
          "gene_symbol": "ENSG00000237188",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.258+12496C>T",
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        }
      ],
      "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
}