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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: 5-146120433-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=146120433&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "5",
      "pos": 146120433,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000394434.7",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 31,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3263G>A",
          "hgvs_p": "p.Arg1088Lys",
          "transcript": "NM_020117.11",
          "protein_id": "NP_064502.9",
          "transcript_support_level": null,
          "aa_start": 1088,
          "aa_end": null,
          "aa_length": 1176,
          "cds_start": 3263,
          "cds_end": null,
          "cds_length": 3531,
          "cdna_start": 3420,
          "cdna_end": null,
          "cdna_length": 4760,
          "mane_select": "ENST00000394434.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 31,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3263G>A",
          "hgvs_p": "p.Arg1088Lys",
          "transcript": "ENST00000394434.7",
          "protein_id": "ENSP00000377954.2",
          "transcript_support_level": 1,
          "aa_start": 1088,
          "aa_end": null,
          "aa_length": 1176,
          "cds_start": 3263,
          "cds_end": null,
          "cds_length": 3531,
          "cdna_start": 3420,
          "cdna_end": null,
          "cdna_length": 4760,
          "mane_select": "NM_020117.11",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 31,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3260G>A",
          "hgvs_p": "p.Arg1087Lys",
          "transcript": "ENST00000674398.1",
          "protein_id": "ENSP00000501476.1",
          "transcript_support_level": null,
          "aa_start": 1087,
          "aa_end": null,
          "aa_length": 1175,
          "cds_start": 3260,
          "cds_end": null,
          "cds_length": 3528,
          "cdna_start": 3437,
          "cdna_end": null,
          "cdna_length": 4768,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 31,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3227G>A",
          "hgvs_p": "p.Arg1076Lys",
          "transcript": "ENST00000674290.1",
          "protein_id": "ENSP00000501435.1",
          "transcript_support_level": null,
          "aa_start": 1076,
          "aa_end": null,
          "aa_length": 1164,
          "cds_start": 3227,
          "cds_end": null,
          "cds_length": 3495,
          "cdna_start": 3394,
          "cdna_end": null,
          "cdna_length": 7202,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 30,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3182G>A",
          "hgvs_p": "p.Arg1061Lys",
          "transcript": "NM_016460.4",
          "protein_id": "NP_057544.2",
          "transcript_support_level": null,
          "aa_start": 1061,
          "aa_end": null,
          "aa_length": 1149,
          "cds_start": 3182,
          "cds_end": null,
          "cds_length": 3450,
          "cdna_start": 3339,
          "cdna_end": null,
          "cdna_length": 4679,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 30,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3182G>A",
          "hgvs_p": "p.Arg1061Lys",
          "transcript": "ENST00000674447.1",
          "protein_id": "ENSP00000501376.1",
          "transcript_support_level": null,
          "aa_start": 1061,
          "aa_end": null,
          "aa_length": 1149,
          "cds_start": 3182,
          "cds_end": null,
          "cds_length": 3450,
          "cdna_start": 3339,
          "cdna_end": null,
          "cdna_length": 7147,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 30,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3125G>A",
          "hgvs_p": "p.Arg1042Lys",
          "transcript": "NM_001317964.2",
          "protein_id": "NP_001304893.1",
          "transcript_support_level": null,
          "aa_start": 1042,
          "aa_end": null,
          "aa_length": 1130,
          "cds_start": 3125,
          "cds_end": null,
          "cds_length": 3393,
          "cdna_start": 3282,
          "cdna_end": null,
          "cdna_length": 4622,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 30,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3125G>A",
          "hgvs_p": "p.Arg1042Lys",
          "transcript": "ENST00000674270.1",
          "protein_id": "ENSP00000501365.1",
          "transcript_support_level": null,
          "aa_start": 1042,
          "aa_end": null,
          "aa_length": 1130,
          "cds_start": 3125,
          "cds_end": null,
          "cds_length": 3393,
          "cdna_start": 3282,
          "cdna_end": null,
          "cdna_length": 7090,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 30,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3101G>A",
          "hgvs_p": "p.Arg1034Lys",
          "transcript": "NM_001317965.2",
          "protein_id": "NP_001304894.1",
          "transcript_support_level": null,
          "aa_start": 1034,
          "aa_end": null,
          "aa_length": 1122,
          "cds_start": 3101,
          "cds_end": null,
          "cds_length": 3369,
          "cdna_start": 3301,
          "cdna_end": null,
          "cdna_length": 4641,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 30,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3101G>A",
          "hgvs_p": "p.Arg1034Lys",
          "transcript": "ENST00000510191.5",
          "protein_id": "ENSP00000426005.1",
          "transcript_support_level": 2,
          "aa_start": 1034,
          "aa_end": null,
          "aa_length": 1122,
          "cds_start": 3101,
          "cds_end": null,
          "cds_length": 3369,
          "cdna_start": 3274,
          "cdna_end": null,
          "cdna_length": 3737,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 31,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3101G>A",
          "hgvs_p": "p.Arg1034Lys",
          "transcript": "ENST00000674174.1",
          "protein_id": "ENSP00000501434.1",
          "transcript_support_level": null,
          "aa_start": 1034,
          "aa_end": null,
          "aa_length": 1122,
          "cds_start": 3101,
          "cds_end": null,
          "cds_length": 3369,
          "cdna_start": 3332,
          "cdna_end": null,
          "cdna_length": 7140,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 31,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
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          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3098G>A",
          "hgvs_p": "p.Arg1033Lys",
          "transcript": "ENST00000674277.1",
          "protein_id": "ENSP00000501510.1",
          "transcript_support_level": null,
          "aa_start": 1033,
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          "aa_length": 1121,
          "cds_start": 3098,
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          "cdna_start": 3338,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 29,
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          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.2882G>A",
          "hgvs_p": "p.Arg961Lys",
          "transcript": "ENST00000674158.1",
          "protein_id": "ENSP00000501474.1",
          "transcript_support_level": null,
          "aa_start": 961,
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          "cds_start": 2882,
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          "cdna_start": 3374,
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          "biotype": null,
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        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 30,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.2807G>A",
          "hgvs_p": "p.Arg936Lys",
          "transcript": "ENST00000674191.1",
          "protein_id": "ENSP00000501478.1",
          "transcript_support_level": null,
          "aa_start": 936,
          "aa_end": null,
          "aa_length": 1024,
          "cds_start": 2807,
          "cds_end": null,
          "cds_length": 3075,
          "cdna_start": 3172,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
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          ],
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          "intron_rank": null,
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          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "c.3101G>A",
          "hgvs_p": "p.Arg1034Lys",
          "transcript": "XM_011537656.4",
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          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "n.3693G>A",
          "hgvs_p": null,
          "transcript": "ENST00000504323.6",
          "protein_id": null,
          "transcript_support_level": 3,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
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          "cdna_length": 4156,
          "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": 13,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "n.6145G>A",
          "hgvs_p": null,
          "transcript": "ENST00000506231.6",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 9953,
          "mane_select": null,
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          "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": 31,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "n.*1701G>A",
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "n.*1067G>A",
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          "transcript": "ENST00000674181.1",
          "protein_id": "ENSP00000501475.1",
          "transcript_support_level": null,
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          "cdna_length": 5318,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 30,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARS1",
          "gene_hgnc_id": 6512,
          "hgvs_c": "n.6050G>A",
          "hgvs_p": null,
          "transcript": "ENST00000674218.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": 9858,
          "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": 30,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
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        },
        {
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          "consequences": [
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          "gene_symbol": "ENSG00000251556",
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          "transcript": "ENST00000514002.1",
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        }
      ],
      "gene_symbol": "LARS1",
      "gene_hgnc_id": 6512,
      "dbsnp": "rs10988",
      "frequency_reference_population": 0.2747827,
      "hom_count_reference_population": 64821,
      "allele_count_reference_population": 443064,
      "gnomad_exomes_af": 0.279989,
      "gnomad_genomes_af": 0.224769,
      "gnomad_exomes_ac": 408891,
      "gnomad_genomes_ac": 34173,
      "gnomad_exomes_homalt": 59976,
      "gnomad_genomes_homalt": 4845,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.0032483041286468506,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.092,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.1502,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.37,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 4.996,
      "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": -20,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
      "acmg_by_gene": [
        {
          "score": -20,
          "benign_score": 20,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000394434.7",
          "gene_symbol": "LARS1",
          "hgnc_id": 6512,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.3263G>A",
          "hgvs_p": "p.Arg1088Lys"
        },
        {
          "score": -20,
          "benign_score": 20,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000514002.1",
          "gene_symbol": "ENSG00000251556",
          "hgnc_id": null,
          "effects": [
            "downstream_gene_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.*21C>T",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "not provided,not specified",
      "clinvar_classification": "Benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "B:2",
      "phenotype_combined": "not specified|not provided",
      "pathogenicity_classification_combined": "Benign",
      "custom_annotations": null
    }
  ],
  "message": null
}