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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: 11-72814482-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=72814482&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "11",
      "pos": 72814482,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "NM_033388.2",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "NM_033388.2",
          "protein_id": "NP_203746.1",
          "transcript_support_level": null,
          "aa_start": 13,
          "aa_end": null,
          "aa_length": 619,
          "cds_start": 37,
          "cds_end": null,
          "cds_length": 1860,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000321297.10",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_033388.2"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "ENST00000321297.10",
          "protein_id": "ENSP00000326340.5",
          "transcript_support_level": 1,
          "aa_start": 13,
          "aa_end": null,
          "aa_length": 619,
          "cds_start": 37,
          "cds_end": null,
          "cds_length": 1860,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_033388.2",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000321297.10"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "ENST00000534905.5",
          "protein_id": "ENSP00000441189.1",
          "transcript_support_level": 1,
          "aa_start": 13,
          "aa_end": null,
          "aa_length": 164,
          "cds_start": 37,
          "cds_end": null,
          "cds_length": 495,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000534905.5"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "ENST00000540567.1",
          "protein_id": "ENSP00000443569.1",
          "transcript_support_level": 1,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 116,
          "cds_start": 49,
          "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": "ENST00000540567.1"
        },
        {
          "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": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "n.64C>T",
          "hgvs_p": null,
          "transcript": "ENST00000439504.6",
          "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": "ENST00000439504.6"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "ENST00000867653.1",
          "protein_id": "ENSP00000537712.1",
          "transcript_support_level": null,
          "aa_start": 13,
          "aa_end": null,
          "aa_length": 616,
          "cds_start": 37,
          "cds_end": null,
          "cds_length": 1851,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000867653.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "ENST00000867652.1",
          "protein_id": "ENSP00000537711.1",
          "transcript_support_level": null,
          "aa_start": 13,
          "aa_end": null,
          "aa_length": 598,
          "cds_start": 37,
          "cds_end": null,
          "cds_length": 1797,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000867652.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "ENST00000949596.1",
          "protein_id": "ENSP00000619655.1",
          "transcript_support_level": null,
          "aa_start": 13,
          "aa_end": null,
          "aa_length": 595,
          "cds_start": 37,
          "cds_end": null,
          "cds_length": 1788,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000949596.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "ENST00000949594.1",
          "protein_id": "ENSP00000619653.1",
          "transcript_support_level": null,
          "aa_start": 13,
          "aa_end": null,
          "aa_length": 581,
          "cds_start": 37,
          "cds_end": null,
          "cds_length": 1746,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000949594.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "ENST00000914046.1",
          "protein_id": "ENSP00000584105.1",
          "transcript_support_level": null,
          "aa_start": 13,
          "aa_end": null,
          "aa_length": 567,
          "cds_start": 37,
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          "cds_length": 1704,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000914046.1"
        },
        {
          "aa_ref": "R",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "ENST00000914047.1",
          "protein_id": "ENSP00000584106.1",
          "transcript_support_level": null,
          "aa_start": 13,
          "aa_end": null,
          "aa_length": 560,
          "cds_start": 37,
          "cds_end": null,
          "cds_length": 1683,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000914047.1"
        },
        {
          "aa_ref": "R",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 1,
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          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "ENST00000949597.1",
          "protein_id": "ENSP00000619656.1",
          "transcript_support_level": null,
          "aa_start": 13,
          "aa_end": null,
          "aa_length": 546,
          "cds_start": 37,
          "cds_end": null,
          "cds_length": 1641,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
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        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
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          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "ENST00000949595.1",
          "protein_id": "ENSP00000619654.1",
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          "cds_start": 37,
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          "cds_length": 1386,
          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000949595.1"
        },
        {
          "aa_ref": "R",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "XM_005274376.6",
          "protein_id": "XP_005274433.1",
          "transcript_support_level": null,
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          "cds_start": 37,
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        {
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          ],
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          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "XM_006718732.3",
          "protein_id": "XP_006718795.1",
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          "aa_end": null,
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          "cds_length": 1797,
          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "XM_006718732.3"
        },
        {
          "aa_ref": "R",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "XM_011545332.2",
          "protein_id": "XP_011543634.1",
          "transcript_support_level": null,
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          "aa_length": 581,
          "cds_start": 37,
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        },
        {
          "aa_ref": "R",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
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          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "XM_047427840.1",
          "protein_id": "XP_047283796.1",
          "transcript_support_level": null,
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        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "XM_047427841.1",
          "protein_id": "XP_047283797.1",
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        },
        {
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          "protein_coding": true,
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          "consequences": [
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          ],
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          "exon_count": 11,
          "intron_rank": null,
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          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys",
          "transcript": "XM_006718733.4",
          "protein_id": "XP_006718796.1",
          "transcript_support_level": null,
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          "cds_start": 37,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_006718733.4"
        },
        {
          "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": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "c.-402C>T",
          "hgvs_p": null,
          "transcript": "NM_001318766.2",
          "protein_id": "NP_001305695.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 513,
          "cds_start": null,
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          "cds_length": 1542,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001318766.2"
        },
        {
          "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": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "n.37C>T",
          "hgvs_p": null,
          "transcript": "ENST00000435507.6",
          "protein_id": "ENSP00000400705.2",
          "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": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000435507.6"
        },
        {
          "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": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "n.58C>T",
          "hgvs_p": null,
          "transcript": "ENST00000537143.5",
          "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": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000537143.5"
        },
        {
          "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": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "n.58C>T",
          "hgvs_p": null,
          "transcript": "ENST00000542908.5",
          "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": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000542908.5"
        },
        {
          "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": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATG16L2",
          "gene_hgnc_id": 25464,
          "hgvs_c": "n.37C>T",
          "hgvs_p": null,
          "transcript": "ENST00000544490.5",
          "protein_id": "ENSP00000442635.1",
          "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": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000544490.5"
        }
      ],
      "gene_symbol": "ATG16L2",
      "gene_hgnc_id": 25464,
      "dbsnp": "rs774060355",
      "frequency_reference_population": null,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 0,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.048225343227386475,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.078,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.1297,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.43,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.006,
      "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": -2,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "PM2,BP4_Strong",
      "acmg_by_gene": [
        {
          "score": -2,
          "benign_score": 4,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Strong"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_033388.2",
          "gene_symbol": "ATG16L2",
          "hgnc_id": 25464,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.37C>T",
          "hgvs_p": "p.Arg13Cys"
        }
      ],
      "clinvar_disease": "not specified",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "not specified",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}