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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: 1-171319908-C-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=171319908&ref=C&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 171319908,
      "ref": "C",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_002022.3",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "NM_002022.3",
          "protein_id": "NP_002013.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 558,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1677,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000367749.4",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_002022.3"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "ENST00000367749.4",
          "protein_id": "ENSP00000356723.3",
          "transcript_support_level": 1,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 558,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1677,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_002022.3",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000367749.4"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "ENST00000853715.1",
          "protein_id": "ENSP00000523774.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 558,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1677,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853715.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "ENST00000853716.1",
          "protein_id": "ENSP00000523775.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 558,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1677,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853716.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "ENST00000853711.1",
          "protein_id": "ENSP00000523770.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 495,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1488,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853711.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "ENST00000853710.1",
          "protein_id": "ENSP00000523769.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 417,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1254,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853710.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "ENST00000853714.1",
          "protein_id": "ENSP00000523773.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 393,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1182,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853714.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "ENST00000853712.1",
          "protein_id": "ENSP00000523771.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 391,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1176,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853712.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "ENST00000919758.1",
          "protein_id": "ENSP00000589817.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 381,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1146,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000919758.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "ENST00000853709.1",
          "protein_id": "ENSP00000523768.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 326,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 981,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853709.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "ENST00000959334.1",
          "protein_id": "ENSP00000629393.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 326,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 981,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000959334.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "ENST00000853713.1",
          "protein_id": "ENSP00000523772.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 318,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 957,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853713.1"
        },
        {
          "aa_ref": "P",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "ENST00000959333.1",
          "protein_id": "ENSP00000629392.1",
          "transcript_support_level": null,
          "aa_start": 28,
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          "cds_start": 83,
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          "cds_length": 792,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000959333.1"
        },
        {
          "aa_ref": "P",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "XM_005245046.4",
          "protein_id": "XP_005245103.1",
          "transcript_support_level": null,
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          "aa_length": 495,
          "cds_start": 83,
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          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
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        },
        {
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
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          "exon_count": 10,
          "intron_rank": null,
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          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "XM_011509347.3",
          "protein_id": "XP_011507649.1",
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          "cds_start": 83,
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          "cds_length": 1410,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "XM_011509347.3"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "XM_047416219.1",
          "protein_id": "XP_047272175.1",
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          "aa_start": 28,
          "aa_end": null,
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          "cds_start": 83,
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          "cdna_start": null,
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          "cdna_length": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "P",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "XM_006711243.4",
          "protein_id": "XP_006711306.1",
          "transcript_support_level": null,
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          "cds_start": 83,
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          "biotype": "protein_coding",
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        {
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          "intron_rank": null,
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          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "XM_005245048.4",
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          "cdna_start": null,
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          "biotype": "protein_coding",
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        },
        {
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          "protein_coding": true,
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          "intron_rank": null,
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          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
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          "transcript": "XM_047416228.1",
          "protein_id": "XP_047272184.1",
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          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "XM_047416228.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His",
          "transcript": "XM_047416232.1",
          "protein_id": "XP_047272188.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 278,
          "cds_start": 83,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "XM_047416232.1"
        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.-18-3096C>A",
          "hgvs_p": null,
          "transcript": "XM_005245045.4",
          "protein_id": "XP_005245102.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 508,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1527,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_005245045.4"
        },
        {
          "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": 8,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "c.-109+3581C>A",
          "hgvs_p": null,
          "transcript": "XM_011509348.3",
          "protein_id": "XP_011507650.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 415,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1248,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_011509348.3"
        },
        {
          "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": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "n.413C>A",
          "hgvs_p": null,
          "transcript": "ENST00000475780.5",
          "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": "pseudogene",
          "feature": "ENST00000475780.5"
        },
        {
          "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": 2,
          "intron_rank_end": null,
          "gene_symbol": "FMO4",
          "gene_hgnc_id": 3772,
          "hgvs_c": "n.349-3096C>A",
          "hgvs_p": null,
          "transcript": "ENST00000497228.5",
          "protein_id": null,
          "transcript_support_level": 5,
          "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": "ENST00000497228.5"
        }
      ],
      "gene_symbol": "FMO4",
      "gene_hgnc_id": 3772,
      "dbsnp": "rs866374389",
      "frequency_reference_population": 0.0000013683484,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 2,
      "gnomad_exomes_af": 0.00000136835,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 2,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.8398199081420898,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.392,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.9348,
      "alphamissense_prediction": "Pathogenic",
      "bayesdelnoaf_score": 0.02,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 6.145,
      "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": 3,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,PP3",
      "acmg_by_gene": [
        {
          "score": 3,
          "benign_score": 0,
          "pathogenic_score": 3,
          "criteria": [
            "PM2",
            "PP3"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_002022.3",
          "gene_symbol": "FMO4",
          "hgnc_id": 3772,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.83C>A",
          "hgvs_p": "p.Pro28His"
        }
      ],
      "clinvar_disease": "Trimethylaminuria",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "Trimethylaminuria",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}