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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: 14-81087993-T-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=81087993&ref=T&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "14",
      "pos": 81087993,
      "ref": "T",
      "alt": "A",
      "effect": "synonymous_variant",
      "transcript": "ENST00000298171.7",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR",
          "gene_hgnc_id": 12373,
          "hgvs_c": "c.357T>A",
          "hgvs_p": "p.Pro119Pro",
          "transcript": "NM_000369.5",
          "protein_id": "NP_000360.2",
          "transcript_support_level": null,
          "aa_start": 119,
          "aa_end": null,
          "aa_length": 764,
          "cds_start": 357,
          "cds_end": null,
          "cds_length": 2295,
          "cdna_start": 417,
          "cdna_end": null,
          "cdna_length": 4308,
          "mane_select": "ENST00000298171.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR",
          "gene_hgnc_id": 12373,
          "hgvs_c": "c.357T>A",
          "hgvs_p": "p.Pro119Pro",
          "transcript": "ENST00000298171.7",
          "protein_id": "ENSP00000298171.2",
          "transcript_support_level": 1,
          "aa_start": 119,
          "aa_end": null,
          "aa_length": 764,
          "cds_start": 357,
          "cds_end": null,
          "cds_length": 2295,
          "cdna_start": 417,
          "cdna_end": null,
          "cdna_length": 4308,
          "mane_select": "NM_000369.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR",
          "gene_hgnc_id": 12373,
          "hgvs_c": "c.357T>A",
          "hgvs_p": "p.Pro119Pro",
          "transcript": "ENST00000554435.1",
          "protein_id": "ENSP00000450549.1",
          "transcript_support_level": 1,
          "aa_start": 119,
          "aa_end": null,
          "aa_length": 274,
          "cds_start": 357,
          "cds_end": null,
          "cds_length": 825,
          "cdna_start": 383,
          "cdna_end": null,
          "cdna_length": 1089,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR",
          "gene_hgnc_id": 12373,
          "hgvs_c": "c.357T>A",
          "hgvs_p": "p.Pro119Pro",
          "transcript": "ENST00000342443.10",
          "protein_id": "ENSP00000340113.6",
          "transcript_support_level": 1,
          "aa_start": 119,
          "aa_end": null,
          "aa_length": 253,
          "cds_start": 357,
          "cds_end": null,
          "cds_length": 762,
          "cdna_start": 607,
          "cdna_end": null,
          "cdna_length": 1281,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR",
          "gene_hgnc_id": 12373,
          "hgvs_c": "c.357T>A",
          "hgvs_p": "p.Pro119Pro",
          "transcript": "ENST00000554263.5",
          "protein_id": "ENSP00000451202.1",
          "transcript_support_level": 1,
          "aa_start": 119,
          "aa_end": null,
          "aa_length": 231,
          "cds_start": 357,
          "cds_end": null,
          "cds_length": 696,
          "cdna_start": 383,
          "cdna_end": null,
          "cdna_length": 1184,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR",
          "gene_hgnc_id": 12373,
          "hgvs_c": "c.357T>A",
          "hgvs_p": "p.Pro119Pro",
          "transcript": "ENST00000541158.6",
          "protein_id": "ENSP00000441235.2",
          "transcript_support_level": 5,
          "aa_start": 119,
          "aa_end": null,
          "aa_length": 764,
          "cds_start": 357,
          "cds_end": null,
          "cds_length": 2295,
          "cdna_start": 679,
          "cdna_end": null,
          "cdna_length": 4566,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR",
          "gene_hgnc_id": 12373,
          "hgvs_c": "c.357T>A",
          "hgvs_p": "p.Pro119Pro",
          "transcript": "NM_001142626.3",
          "protein_id": "NP_001136098.1",
          "transcript_support_level": null,
          "aa_start": 119,
          "aa_end": null,
          "aa_length": 274,
          "cds_start": 357,
          "cds_end": null,
          "cds_length": 825,
          "cdna_start": 417,
          "cdna_end": null,
          "cdna_length": 1144,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR",
          "gene_hgnc_id": 12373,
          "hgvs_c": "c.357T>A",
          "hgvs_p": "p.Pro119Pro",
          "transcript": "NM_001018036.3",
          "protein_id": "NP_001018046.1",
          "transcript_support_level": null,
          "aa_start": 119,
          "aa_end": null,
          "aa_length": 253,
          "cds_start": 357,
          "cds_end": null,
          "cds_length": 762,
          "cdna_start": 417,
          "cdna_end": null,
          "cdna_length": 1081,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR",
          "gene_hgnc_id": 12373,
          "hgvs_c": "c.78T>A",
          "hgvs_p": "p.Pro26Pro",
          "transcript": "XM_011537119.3",
          "protein_id": "XP_011535421.1",
          "transcript_support_level": null,
          "aa_start": 26,
          "aa_end": null,
          "aa_length": 671,
          "cds_start": 78,
          "cds_end": null,
          "cds_length": 2016,
          "cdna_start": 147,
          "cdna_end": null,
          "cdna_length": 4038,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR",
          "gene_hgnc_id": 12373,
          "hgvs_c": "n.*67T>A",
          "hgvs_p": null,
          "transcript": "ENST00000555326.5",
          "protein_id": "ENSP00000451092.1",
          "transcript_support_level": 4,
          "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": 557,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR",
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          "hgvs_c": "n.275T>A",
          "hgvs_p": null,
          "transcript": "ENST00000636454.1",
          "protein_id": null,
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1606,
          "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": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR-AS1",
          "gene_hgnc_id": 58172,
          "hgvs_c": "n.13599A>T",
          "hgvs_p": null,
          "transcript": "XR_007064286.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "mane_select": null,
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          "biotype": null,
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        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR-AS1",
          "gene_hgnc_id": 58172,
          "hgvs_c": "n.12772A>T",
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          "transcript": "XR_007064287.1",
          "protein_id": null,
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          "cdna_length": 17681,
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        },
        {
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          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR-AS1",
          "gene_hgnc_id": 58172,
          "hgvs_c": "n.12730A>T",
          "hgvs_p": null,
          "transcript": "XR_007064288.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
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          "cdna_length": 17639,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
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          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR-AS1",
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          "hgvs_c": "n.13968A>T",
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          "feature": null
        },
        {
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR-AS1",
          "gene_hgnc_id": 58172,
          "hgvs_c": "n.13677A>T",
          "hgvs_p": null,
          "transcript": "XR_007064291.1",
          "protein_id": null,
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          "cdna_length": 18586,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSHR",
          "gene_hgnc_id": 12373,
          "hgvs_c": "n.*67T>A",
          "hgvs_p": null,
          "transcript": "ENST00000555326.5",
          "protein_id": "ENSP00000451092.1",
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          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000284959",
          "gene_hgnc_id": 58172,
          "hgvs_c": "n.905-341A>T",
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          "transcript": "ENST00000646052.2",
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        },
        {
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          "consequences": [
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          ],
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          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000284959",
          "gene_hgnc_id": 58172,
          "hgvs_c": "n.1001-341A>T",
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          "transcript": "ENST00000646928.1",
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        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 8,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000284959",
          "gene_hgnc_id": 58172,
          "hgvs_c": "n.905-341A>T",
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          "transcript": "ENST00000652775.1",
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          "cdna_length": 1510,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 4,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000284959",
          "gene_hgnc_id": 58172,
          "hgvs_c": "n.720+5589A>T",
          "hgvs_p": null,
          "transcript": "ENST00000654681.1",
          "protein_id": null,
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          ],
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          "gene_symbol": "TSHR-AS1",
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        },
        {
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          ],
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          "gene_symbol": "TSHR-AS1",
          "gene_hgnc_id": 58172,
          "hgvs_c": "n.882-341A>T",
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          "transcript": "XR_007064290.1",
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          "cds_length": null,
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          "cdna_length": 10308,
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          "feature": null
        }
      ],
      "gene_symbol": "TSHR",
      "gene_hgnc_id": 12373,
      "dbsnp": "rs144084915",
      "frequency_reference_population": 0.002544717,
      "hom_count_reference_population": 11,
      "allele_count_reference_population": 4107,
      "gnomad_exomes_af": 0.00263405,
      "gnomad_genomes_af": 0.00168741,
      "gnomad_exomes_ac": 3850,
      "gnomad_genomes_ac": 257,
      "gnomad_exomes_homalt": 11,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.44999998807907104,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.45,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.376,
      "phylop100way_prediction": "Benign",
      "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": -12,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Moderate,BP6,BP7,BS1,BS2",
      "acmg_by_gene": [
        {
          "score": -12,
          "benign_score": 12,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Moderate",
            "BP6",
            "BP7",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000298171.7",
          "gene_symbol": "TSHR",
          "hgnc_id": 12373,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.357T>A",
          "hgvs_p": "p.Pro119Pro"
        },
        {
          "score": -7,
          "benign_score": 7,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Moderate",
            "BP6",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "XR_007064286.1",
          "gene_symbol": "TSHR-AS1",
          "hgnc_id": 58172,
          "effects": [
            "non_coding_transcript_exon_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.13599A>T",
          "hgvs_p": null
        },
        {
          "score": -7,
          "benign_score": 7,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Moderate",
            "BP6",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000646052.2",
          "gene_symbol": "ENSG00000284959",
          "hgnc_id": 58172,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.905-341A>T",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "Familial hyperthyroidism due to mutations in TSH receptor,Hypothyroidism due to TSH receptor mutations,not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:2 LB:2 B:3",
      "phenotype_combined": "Hypothyroidism due to TSH receptor mutations|not specified|not provided|Familial hyperthyroidism due to mutations in TSH receptor",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}