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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: 1-11790843-G-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=11790843&ref=G&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 11790843,
      "ref": "G",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "ENST00000376590.9",
      "consequences": [
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1808C>G",
          "hgvs_p": "p.Ser603Cys",
          "transcript": "NM_005957.5",
          "protein_id": "NP_005948.3",
          "transcript_support_level": null,
          "aa_start": 603,
          "aa_end": null,
          "aa_length": 656,
          "cds_start": 1808,
          "cds_end": null,
          "cds_length": 1971,
          "cdna_start": 1898,
          "cdna_end": null,
          "cdna_length": 7018,
          "mane_select": "ENST00000376590.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1808C>G",
          "hgvs_p": "p.Ser603Cys",
          "transcript": "ENST00000376590.9",
          "protein_id": "ENSP00000365775.3",
          "transcript_support_level": 1,
          "aa_start": 603,
          "aa_end": null,
          "aa_length": 656,
          "cds_start": 1808,
          "cds_end": null,
          "cds_length": 1971,
          "cdna_start": 1898,
          "cdna_end": null,
          "cdna_length": 7018,
          "mane_select": "NM_005957.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1928C>G",
          "hgvs_p": "p.Ser643Cys",
          "transcript": "ENST00000423400.7",
          "protein_id": "ENSP00000398908.3",
          "transcript_support_level": 1,
          "aa_start": 643,
          "aa_end": null,
          "aa_length": 696,
          "cds_start": 1928,
          "cds_end": null,
          "cds_length": 2091,
          "cdna_start": 1940,
          "cdna_end": null,
          "cdna_length": 2715,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1808C>G",
          "hgvs_p": "p.Ser603Cys",
          "transcript": "ENST00000376592.6",
          "protein_id": "ENSP00000365777.1",
          "transcript_support_level": 1,
          "aa_start": 603,
          "aa_end": null,
          "aa_length": 656,
          "cds_start": 1808,
          "cds_end": null,
          "cds_length": 1971,
          "cdna_start": 3258,
          "cdna_end": null,
          "cdna_length": 8378,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1931C>G",
          "hgvs_p": "p.Ser644Cys",
          "transcript": "NM_001330358.2",
          "protein_id": "NP_001317287.1",
          "transcript_support_level": null,
          "aa_start": 644,
          "aa_end": null,
          "aa_length": 697,
          "cds_start": 1931,
          "cds_end": null,
          "cds_length": 2094,
          "cdna_start": 1954,
          "cdna_end": null,
          "cdna_length": 7074,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1931C>G",
          "hgvs_p": "p.Ser644Cys",
          "transcript": "ENST00000376583.7",
          "protein_id": "ENSP00000365767.3",
          "transcript_support_level": 5,
          "aa_start": 644,
          "aa_end": null,
          "aa_length": 697,
          "cds_start": 1931,
          "cds_end": null,
          "cds_length": 2094,
          "cdna_start": 1931,
          "cdna_end": null,
          "cdna_length": 7044,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1931C>G",
          "hgvs_p": "p.Ser644Cys",
          "transcript": "ENST00000376585.6",
          "protein_id": "ENSP00000365770.1",
          "transcript_support_level": 5,
          "aa_start": 644,
          "aa_end": null,
          "aa_length": 697,
          "cds_start": 1931,
          "cds_end": null,
          "cds_length": 2094,
          "cdna_start": 2983,
          "cdna_end": null,
          "cdna_length": 8094,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1928C>G",
          "hgvs_p": "p.Ser643Cys",
          "transcript": "NM_001410750.1",
          "protein_id": "NP_001397679.1",
          "transcript_support_level": null,
          "aa_start": 643,
          "aa_end": null,
          "aa_length": 696,
          "cds_start": 1928,
          "cds_end": null,
          "cds_length": 2091,
          "cdna_start": 1951,
          "cdna_end": null,
          "cdna_length": 7071,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1073C>G",
          "hgvs_p": "p.Ser358Cys",
          "transcript": "ENST00000641820.1",
          "protein_id": "ENSP00000492937.1",
          "transcript_support_level": null,
          "aa_start": 358,
          "aa_end": null,
          "aa_length": 411,
          "cds_start": 1073,
          "cds_end": null,
          "cds_length": 1236,
          "cdna_start": 1368,
          "cdna_end": null,
          "cdna_length": 1569,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1808C>G",
          "hgvs_p": "p.Ser603Cys",
          "transcript": "XM_005263462.5",
          "protein_id": "XP_005263519.1",
          "transcript_support_level": null,
          "aa_start": 603,
          "aa_end": null,
          "aa_length": 656,
          "cds_start": 1808,
          "cds_end": null,
          "cds_length": 1971,
          "cdna_start": 1895,
          "cdna_end": null,
          "cdna_length": 7015,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1808C>G",
          "hgvs_p": "p.Ser603Cys",
          "transcript": "XM_047421178.1",
          "protein_id": "XP_047277134.1",
          "transcript_support_level": null,
          "aa_start": 603,
          "aa_end": null,
          "aa_length": 656,
          "cds_start": 1808,
          "cds_end": null,
          "cds_length": 1971,
          "cdna_start": 2436,
          "cdna_end": null,
          "cdna_length": 7556,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1562C>G",
          "hgvs_p": "p.Ser521Cys",
          "transcript": "XM_005263463.5",
          "protein_id": "XP_005263520.1",
          "transcript_support_level": null,
          "aa_start": 521,
          "aa_end": null,
          "aa_length": 574,
          "cds_start": 1562,
          "cds_end": null,
          "cds_length": 1725,
          "cdna_start": 1678,
          "cdna_end": null,
          "cdna_length": 6798,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "n.*267C>G",
          "hgvs_p": null,
          "transcript": "ENST00000641446.1",
          "protein_id": "ENSP00000493262.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 2820,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "n.*1320C>G",
          "hgvs_p": null,
          "transcript": "ENST00000641747.1",
          "protein_id": "ENSP00000493116.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3227,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "n.2177C>G",
          "hgvs_p": null,
          "transcript": "ENST00000641759.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "cds_start": -4,
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          "cdna_start": null,
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          "cdna_length": 2454,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "n.*267C>G",
          "hgvs_p": null,
          "transcript": "ENST00000641446.1",
          "protein_id": "ENSP00000493262.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2820,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "n.*1320C>G",
          "hgvs_p": null,
          "transcript": "ENST00000641747.1",
          "protein_id": "ENSP00000493116.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
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          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 3227,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": 10,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1753-127C>G",
          "hgvs_p": null,
          "transcript": "ENST00000641407.1",
          "protein_id": "ENSP00000493098.1",
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          "cds_start": -4,
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          "cds_length": 1929,
          "cdna_start": null,
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          "cdna_length": 2387,
          "mane_select": null,
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": 10,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "n.2270-127C>G",
          "hgvs_p": null,
          "transcript": "ENST00000641805.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 2945,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": 11,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1876-127C>G",
          "hgvs_p": null,
          "transcript": "XM_011541496.4",
          "protein_id": "XP_011539798.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 683,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2052,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6892,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": 11,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1873-127C>G",
          "hgvs_p": null,
          "transcript": "XM_047421174.1",
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          "transcript": "XM_047421181.1",
          "protein_id": "XP_047277137.1",
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        }
      ],
      "gene_symbol": "MTHFR",
      "gene_hgnc_id": 7436,
      "dbsnp": "rs758206023",
      "frequency_reference_population": 0.000008054572,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 13,
      "gnomad_exomes_af": 0.00000820855,
      "gnomad_genomes_af": 0.00000657462,
      "gnomad_exomes_ac": 12,
      "gnomad_genomes_ac": 1,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.8071596026420593,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.525,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.1835,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.07,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 9.449,
      "phylop100way_prediction": "Pathogenic",
      "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": 4,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,PP3,PP5",
      "acmg_by_gene": [
        {
          "score": 4,
          "benign_score": 0,
          "pathogenic_score": 4,
          "criteria": [
            "PM2",
            "PP3",
            "PP5"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000376590.9",
          "gene_symbol": "MTHFR",
          "hgnc_id": 7436,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1808C>G",
          "hgvs_p": "p.Ser603Cys"
        }
      ],
      "clinvar_disease": "Homocystinuria due to methylene tetrahydrofolate reductase deficiency",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "no assertion criteria provided",
      "clinvar_submissions_summary": "null",
      "phenotype_combined": "Homocystinuria due to methylene tetrahydrofolate reductase deficiency",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}