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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: 6-10528561-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=10528561&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "6",
      "pos": 10528561,
      "ref": "T",
      "alt": "C",
      "effect": "5_prime_UTR_variant",
      "transcript": "NM_001374747.1",
      "consequences": [
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "5_prime_UTR_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "c.-351T>C",
          "hgvs_p": null,
          "transcript": "ENST00000379597.7",
          "protein_id": "ENSP00000368917.3",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 402,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1209,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000379597.7"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "c.-281-70T>C",
          "hgvs_p": null,
          "transcript": "NM_145649.5",
          "protein_id": "NP_663624.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 402,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1209,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000495262.7",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_145649.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "c.-281-70T>C",
          "hgvs_p": null,
          "transcript": "ENST00000495262.7",
          "protein_id": "ENSP00000419411.2",
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 402,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1209,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_145649.5",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000495262.7"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "c.67+19403T>C",
          "hgvs_p": null,
          "transcript": "ENST00000410107.5",
          "protein_id": "ENSP00000386321.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 116,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 351,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000410107.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "n.274-70T>C",
          "hgvs_p": null,
          "transcript": "ENST00000397423.7",
          "protein_id": null,
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000397423.7"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "n.297-70T>C",
          "hgvs_p": null,
          "transcript": "ENST00000474983.5",
          "protein_id": null,
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000474983.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "n.283+35630T>C",
          "hgvs_p": null,
          "transcript": "ENST00000489225.5",
          "protein_id": null,
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000489225.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "n.175+6967T>C",
          "hgvs_p": null,
          "transcript": "ENST00000489819.5",
          "protein_id": null,
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000489819.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "5_prime_UTR_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "c.-351T>C",
          "hgvs_p": null,
          "transcript": "NM_001374747.1",
          "protein_id": "NP_001361676.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 402,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1209,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001374747.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "c.-281-70T>C",
          "hgvs_p": null,
          "transcript": "ENST00000910531.1",
          "protein_id": "ENSP00000580590.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 402,
          "cds_start": null,
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          "cds_length": 1209,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000910531.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 1,
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          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "c.-281-70T>C",
          "hgvs_p": null,
          "transcript": "ENST00000942490.1",
          "protein_id": "ENSP00000612549.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": 402,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1209,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
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          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
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          "hgvs_c": "c.-275-76T>C",
          "hgvs_p": null,
          "transcript": "ENST00000942491.1",
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          "cds_start": null,
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          "cdna_start": null,
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        {
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          ],
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          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "c.-281-70T>C",
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          "transcript": "ENST00000942492.1",
          "protein_id": "ENSP00000612551.1",
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          "cds_start": null,
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        {
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          ],
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          "intron_rank": 2,
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          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "c.-281-70T>C",
          "hgvs_p": null,
          "transcript": "ENST00000910532.1",
          "protein_id": "ENSP00000580591.1",
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          "aa_end": null,
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          "cds_start": null,
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          "cdna_start": null,
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        {
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        {
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          "gene_symbol": "GCNT2",
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          "hgvs_c": "c.-281-70T>C",
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          "transcript": "XM_047418632.1",
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        {
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          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "c.-258-70T>C",
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          "transcript": "XM_005248999.3",
          "protein_id": "XP_005249056.1",
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          "cds_start": null,
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          "cdna_start": null,
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        {
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          "gene_symbol": "GCNT2",
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        {
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          "gene_symbol": "GCNT2",
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          "hgvs_c": "c.-281-70T>C",
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        },
        {
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          ],
          "exon_rank": null,
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          "exon_count": 4,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "n.298-70T>C",
          "hgvs_p": null,
          "transcript": "ENST00000474518.1",
          "protein_id": null,
          "transcript_support_level": 4,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000474518.1"
        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 4,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
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          "hgvs_c": "n.254+901T>C",
          "hgvs_p": null,
          "transcript": "ENST00000475577.5",
          "protein_id": null,
          "transcript_support_level": 4,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "pseudogene",
          "feature": "ENST00000475577.5"
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "n.296-70T>C",
          "hgvs_p": null,
          "transcript": "ENST00000483204.2",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000483204.2"
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "n.469-70T>C",
          "hgvs_p": null,
          "transcript": "ENST00000488742.5",
          "protein_id": null,
          "transcript_support_level": 4,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": null,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000488742.5"
        },
        {
          "aa_ref": null,
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 5,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "n.255-70T>C",
          "hgvs_p": null,
          "transcript": "XR_002956275.2",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "pseudogene",
          "feature": "XR_002956275.2"
        },
        {
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 5,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "GCNT2",
          "gene_hgnc_id": 4204,
          "hgvs_c": "n.255-70T>C",
          "hgvs_p": null,
          "transcript": "XR_926136.3",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
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          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "XR_926136.3"
        }
      ],
      "gene_symbol": "GCNT2",
      "gene_hgnc_id": 4204,
      "dbsnp": "rs560194",
      "frequency_reference_population": 0.5540256,
      "hom_count_reference_population": 54723,
      "allele_count_reference_population": 194135,
      "gnomad_exomes_af": 0.557774,
      "gnomad_genomes_af": 0.549132,
      "gnomad_exomes_ac": 110679,
      "gnomad_genomes_ac": 83456,
      "gnomad_exomes_homalt": 31648,
      "gnomad_genomes_homalt": 23075,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.8100000023841858,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": null,
      "splice_prediction_selected": null,
      "splice_source_selected": null,
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.81,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -1.653,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": null,
      "spliceai_max_prediction": null,
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": -14,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Moderate,BA1",
      "acmg_by_gene": [
        {
          "score": -14,
          "benign_score": 14,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Moderate",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "NM_001374747.1",
          "gene_symbol": "GCNT2",
          "hgnc_id": 4204,
          "effects": [
            "5_prime_UTR_variant"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "c.-351T>C",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "not provided",
      "clinvar_classification": "Benign",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "B:1",
      "phenotype_combined": "not provided",
      "pathogenicity_classification_combined": "Benign",
      "custom_annotations": null
    }
  ],
  "message": null
}