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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: 13-52024837-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=52024837&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "13",
      "pos": 52024837,
      "ref": "T",
      "alt": "C",
      "effect": "synonymous_variant",
      "transcript": "NM_001004127.3",
      "consequences": [
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "c.1107T>C",
          "hgvs_p": "p.Tyr369Tyr",
          "transcript": "NM_001004127.3",
          "protein_id": "NP_001004127.2",
          "transcript_support_level": null,
          "aa_start": 369,
          "aa_end": null,
          "aa_length": 492,
          "cds_start": 1107,
          "cds_end": null,
          "cds_length": 1479,
          "cdna_start": 1128,
          "cdna_end": null,
          "cdna_length": 6510,
          "mane_select": "ENST00000521508.2",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001004127.3"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "c.1107T>C",
          "hgvs_p": "p.Tyr369Tyr",
          "transcript": "ENST00000521508.2",
          "protein_id": "ENSP00000430236.1",
          "transcript_support_level": 1,
          "aa_start": 369,
          "aa_end": null,
          "aa_length": 492,
          "cds_start": 1107,
          "cds_end": null,
          "cds_length": 1479,
          "cdna_start": 1128,
          "cdna_end": null,
          "cdna_length": 6510,
          "mane_select": "NM_001004127.3",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000521508.2"
        },
        {
          "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": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "UTP14C",
          "gene_hgnc_id": 20321,
          "hgvs_c": "c.-587T>C",
          "hgvs_p": null,
          "transcript": "NM_021645.6",
          "protein_id": "NP_067677.4",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 766,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 2301,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5529,
          "mane_select": "ENST00000521776.2",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_021645.6"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "5_prime_UTR_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "UTP14C",
          "gene_hgnc_id": 20321,
          "hgvs_c": "c.-587T>C",
          "hgvs_p": null,
          "transcript": "ENST00000521776.2",
          "protein_id": "ENSP00000428619.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 766,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 2301,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5529,
          "mane_select": "NM_021645.6",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000521776.2"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "c.1107T>C",
          "hgvs_p": "p.Tyr369Tyr",
          "transcript": "ENST00000649340.2",
          "protein_id": "ENSP00000497184.2",
          "transcript_support_level": null,
          "aa_start": 369,
          "aa_end": null,
          "aa_length": 491,
          "cds_start": 1107,
          "cds_end": null,
          "cds_length": 1476,
          "cdna_start": 1128,
          "cdna_end": null,
          "cdna_length": 5097,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000649340.2"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "c.876T>C",
          "hgvs_p": "p.Tyr292Tyr",
          "transcript": "ENST00000681053.1",
          "protein_id": "ENSP00000505307.1",
          "transcript_support_level": null,
          "aa_start": 292,
          "aa_end": null,
          "aa_length": 415,
          "cds_start": 876,
          "cds_end": null,
          "cds_length": 1248,
          "cdna_start": 897,
          "cdna_end": null,
          "cdna_length": 6219,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000681053.1"
        },
        {
          "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": 3,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "c.275+5694T>C",
          "hgvs_p": null,
          "transcript": "ENST00000649708.2",
          "protein_id": "ENSP00000497459.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 117,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 354,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 997,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000649708.2"
        },
        {
          "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": 3,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "c.276-3482T>C",
          "hgvs_p": null,
          "transcript": "ENST00000679544.1",
          "protein_id": "ENSP00000505560.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 113,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 342,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5510,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000679544.1"
        },
        {
          "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": 3,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "c.*1-3485T>C",
          "hgvs_p": null,
          "transcript": "ENST00000681145.1",
          "protein_id": "ENSP00000505163.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 92,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 279,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1520,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000681145.1"
        },
        {
          "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": 2,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "c.45-3482T>C",
          "hgvs_p": null,
          "transcript": "ENST00000523764.1",
          "protein_id": "ENSP00000429497.1",
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 36,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 111,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1404,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000523764.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "n.4043T>C",
          "hgvs_p": null,
          "transcript": "ENST00000519151.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "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": 4574,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000519151.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "n.5411T>C",
          "hgvs_p": null,
          "transcript": "ENST00000649651.2",
          "protein_id": null,
          "transcript_support_level": null,
          "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": 10733,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000649651.2"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "n.*215T>C",
          "hgvs_p": null,
          "transcript": "ENST00000650049.2",
          "protein_id": "ENSP00000497398.2",
          "transcript_support_level": null,
          "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": 1004,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000650049.2"
        },
        {
          "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": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "n.*859T>C",
          "hgvs_p": null,
          "transcript": "ENST00000679359.1",
          "protein_id": "ENSP00000505579.1",
          "transcript_support_level": null,
          "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": 6504,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000679359.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "n.1010T>C",
          "hgvs_p": null,
          "transcript": "ENST00000680058.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": 6332,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000680058.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "n.1234T>C",
          "hgvs_p": null,
          "transcript": "ENST00000680950.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": 6556,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000680950.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "n.*832T>C",
          "hgvs_p": null,
          "transcript": "ENST00000681047.1",
          "protein_id": "ENSP00000505034.1",
          "transcript_support_level": null,
          "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": 6454,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000681047.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "n.*215T>C",
          "hgvs_p": null,
          "transcript": "ENST00000650049.2",
          "protein_id": "ENSP00000497398.2",
          "transcript_support_level": null,
          "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": 1004,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000650049.2"
        },
        {
          "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": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "n.*859T>C",
          "hgvs_p": null,
          "transcript": "ENST00000679359.1",
          "protein_id": "ENSP00000505579.1",
          "transcript_support_level": null,
          "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": 6504,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000679359.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG11",
          "gene_hgnc_id": 32456,
          "hgvs_c": "n.*832T>C",
          "hgvs_p": null,
          "transcript": "ENST00000681047.1",
          "protein_id": "ENSP00000505034.1",
          "transcript_support_level": null,
          "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": 6454,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000681047.1"
        },
        {
          "aa_ref": null,
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          "exon_count": 4,
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          "cdna_length": 6052,
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          "biotype": "pseudogene",
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        {
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          "gene_symbol": "ALG11",
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          "hgvs_c": "n.396-3482T>C",
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          "gene_symbol": "ALG11",
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          "hgvs_c": "n.66-3482T>C",
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          "transcript": "NR_036571.3",
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          "cdna_length": 5347,
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          "biotype": "pseudogene",
          "feature": "NR_036571.3"
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      ],
      "gene_symbol": "ALG11",
      "gene_hgnc_id": 32456,
      "dbsnp": "rs146432805",
      "frequency_reference_population": 0.00045044208,
      "hom_count_reference_population": 7,
      "allele_count_reference_population": 727,
      "gnomad_exomes_af": 0.000439927,
      "gnomad_genomes_af": 0.000551311,
      "gnomad_exomes_ac": 643,
      "gnomad_genomes_ac": 84,
      "gnomad_exomes_homalt": 4,
      "gnomad_genomes_homalt": 3,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.7599999904632568,
      "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": -0.76,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.439,
      "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": -21,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
      "acmg_by_gene": [
        {
          "score": -21,
          "benign_score": 21,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BP7",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "NM_001004127.3",
          "gene_symbol": "ALG11",
          "hgnc_id": 32456,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1107T>C",
          "hgvs_p": "p.Tyr369Tyr"
        },
        {
          "score": -16,
          "benign_score": 16,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "NM_021645.6",
          "gene_symbol": "UTP14C",
          "hgnc_id": 20321,
          "effects": [
            "5_prime_UTR_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.-587T>C",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "ALG11-congenital disorder of glycosylation,not specified",
      "clinvar_classification": "Benign/Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:1 B:2",
      "phenotype_combined": "not specified|ALG11-congenital disorder of glycosylation",
      "pathogenicity_classification_combined": "Benign/Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}
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