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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: 1-44008366-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=44008366&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 44008366,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000372310.8",
      "consequences": [
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.577G>A",
          "hgvs_p": "p.Glu193Lys",
          "transcript": "NM_001024845.3",
          "protein_id": "NP_001020016.1",
          "transcript_support_level": null,
          "aa_start": 193,
          "aa_end": null,
          "aa_length": 633,
          "cds_start": 577,
          "cds_end": null,
          "cds_length": 1902,
          "cdna_start": 819,
          "cdna_end": null,
          "cdna_length": 3206,
          "mane_select": "ENST00000372310.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.577G>A",
          "hgvs_p": "p.Glu193Lys",
          "transcript": "ENST00000372310.8",
          "protein_id": "ENSP00000361384.4",
          "transcript_support_level": 5,
          "aa_start": 193,
          "aa_end": null,
          "aa_length": 633,
          "cds_start": 577,
          "cds_end": null,
          "cds_length": 1902,
          "cdna_start": 819,
          "cdna_end": null,
          "cdna_length": 3206,
          "mane_select": "NM_001024845.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.796G>A",
          "hgvs_p": "p.Glu266Lys",
          "transcript": "ENST00000360584.6",
          "protein_id": "ENSP00000353791.2",
          "transcript_support_level": 1,
          "aa_start": 266,
          "aa_end": null,
          "aa_length": 706,
          "cds_start": 796,
          "cds_end": null,
          "cds_length": 2121,
          "cdna_start": 988,
          "cdna_end": null,
          "cdna_length": 2330,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.634G>A",
          "hgvs_p": "p.Glu212Lys",
          "transcript": "ENST00000357730.6",
          "protein_id": "ENSP00000350362.2",
          "transcript_support_level": 1,
          "aa_start": 212,
          "aa_end": null,
          "aa_length": 652,
          "cds_start": 634,
          "cds_end": null,
          "cds_length": 1959,
          "cdna_start": 826,
          "cdna_end": null,
          "cdna_length": 2168,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.796G>A",
          "hgvs_p": "p.Glu266Lys",
          "transcript": "NM_201649.4",
          "protein_id": "NP_964012.2",
          "transcript_support_level": null,
          "aa_start": 266,
          "aa_end": null,
          "aa_length": 706,
          "cds_start": 796,
          "cds_end": null,
          "cds_length": 2121,
          "cdna_start": 826,
          "cdna_end": null,
          "cdna_length": 3213,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.634G>A",
          "hgvs_p": "p.Glu212Lys",
          "transcript": "NM_006934.4",
          "protein_id": "NP_008865.2",
          "transcript_support_level": null,
          "aa_start": 212,
          "aa_end": null,
          "aa_length": 652,
          "cds_start": 634,
          "cds_end": null,
          "cds_length": 1959,
          "cdna_start": 664,
          "cdna_end": null,
          "cdna_length": 3051,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.589G>A",
          "hgvs_p": "p.Glu197Lys",
          "transcript": "NM_001261380.2",
          "protein_id": "NP_001248309.1",
          "transcript_support_level": null,
          "aa_start": 197,
          "aa_end": null,
          "aa_length": 637,
          "cds_start": 589,
          "cds_end": null,
          "cds_length": 1914,
          "cdna_start": 619,
          "cdna_end": null,
          "cdna_length": 3006,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.577G>A",
          "hgvs_p": "p.Glu193Lys",
          "transcript": "NM_001328629.1",
          "protein_id": "NP_001315558.1",
          "transcript_support_level": null,
          "aa_start": 193,
          "aa_end": null,
          "aa_length": 633,
          "cds_start": 577,
          "cds_end": null,
          "cds_length": 1902,
          "cdna_start": 698,
          "cdna_end": null,
          "cdna_length": 3085,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.577G>A",
          "hgvs_p": "p.Glu193Lys",
          "transcript": "ENST00000673836.1",
          "protein_id": "ENSP00000501314.1",
          "transcript_support_level": null,
          "aa_start": 193,
          "aa_end": null,
          "aa_length": 633,
          "cds_start": 577,
          "cds_end": null,
          "cds_length": 1902,
          "cdna_start": 752,
          "cdna_end": null,
          "cdna_length": 3119,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.514G>A",
          "hgvs_p": "p.Glu172Lys",
          "transcript": "NM_001328627.1",
          "protein_id": "NP_001315556.1",
          "transcript_support_level": null,
          "aa_start": 172,
          "aa_end": null,
          "aa_length": 612,
          "cds_start": 514,
          "cds_end": null,
          "cds_length": 1839,
          "cdna_start": 684,
          "cdna_end": null,
          "cdna_length": 3071,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 5,
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          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.577G>A",
          "hgvs_p": "p.Glu193Lys",
          "transcript": "ENST00000372306.7",
          "protein_id": "ENSP00000361380.3",
          "transcript_support_level": 2,
          "aa_start": 193,
          "aa_end": null,
          "aa_length": 579,
          "cds_start": 577,
          "cds_end": null,
          "cds_length": 1740,
          "cdna_start": 717,
          "cdna_end": null,
          "cdna_length": 1926,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
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          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "SLC6A9",
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          "hgvs_c": "c.382G>A",
          "hgvs_p": "p.Glu128Lys",
          "transcript": "ENST00000372307.7",
          "protein_id": "ENSP00000361381.3",
          "transcript_support_level": 2,
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          "cds_start": 382,
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          "cds_length": 1725,
          "cdna_start": 710,
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          "mane_select": null,
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        {
          "aa_ref": "E",
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          ],
          "exon_rank": 2,
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          "intron_rank": null,
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          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.382G>A",
          "hgvs_p": "p.Glu128Lys",
          "transcript": "NM_001328628.1",
          "protein_id": "NP_001315557.1",
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          "aa_length": 568,
          "cds_start": 382,
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        },
        {
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 3,
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          "intron_rank": null,
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          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.244G>A",
          "hgvs_p": "p.Glu82Lys",
          "transcript": "NM_001328626.2",
          "protein_id": "NP_001315555.1",
          "transcript_support_level": null,
          "aa_start": 82,
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          "cds_start": 244,
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          "cdna_start": 530,
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        },
        {
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        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.244G>A",
          "hgvs_p": "p.Glu82Lys",
          "transcript": "NM_001328630.2",
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        {
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          "intron_rank": null,
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          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.739G>A",
          "hgvs_p": "p.Glu247Lys",
          "transcript": "XM_047428739.1",
          "protein_id": "XP_047284695.1",
          "transcript_support_level": null,
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        {
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        {
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          "gene_symbol": "SLC6A9",
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          "hgvs_c": "c.796G>A",
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        },
        {
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          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.496G>A",
          "hgvs_p": "p.Glu166Lys",
          "transcript": "XM_017002152.3",
          "protein_id": "XP_016857641.1",
          "transcript_support_level": null,
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          "aa_end": null,
          "aa_length": 606,
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          "cdna_length": 2968,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
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          "exon_count": 14,
          "intron_rank": null,
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          "hgvs_p": "p.Glu247Lys",
          "transcript": "XM_047428743.1",
          "protein_id": "XP_047284699.1",
          "transcript_support_level": null,
          "aa_start": 247,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 739,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": 981,
          "cdna_end": null,
          "cdna_length": 2311,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
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          "hgvs_c": "c.577G>A",
          "hgvs_p": "p.Glu193Lys",
          "transcript": "XM_047428744.1",
          "protein_id": "XP_047284700.1",
          "transcript_support_level": null,
          "aa_start": 193,
          "aa_end": null,
          "aa_length": 545,
          "cds_start": 577,
          "cds_end": null,
          "cds_length": 1638,
          "cdna_start": 819,
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          "cdna_length": 2149,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "n.664G>A",
          "hgvs_p": null,
          "transcript": "NR_048548.2",
          "protein_id": null,
          "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": 3047,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "c.*231G>A",
          "hgvs_p": null,
          "transcript": "ENST00000528803.1",
          "protein_id": "ENSP00000435652.1",
          "transcript_support_level": 4,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 133,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 403,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 524,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A9",
          "gene_hgnc_id": 11056,
          "hgvs_c": "n.*149G>A",
          "hgvs_p": null,
          "transcript": "ENST00000492434.6",
          "protein_id": null,
          "transcript_support_level": 3,
          "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": 592,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "SLC6A9",
      "gene_hgnc_id": 11056,
      "dbsnp": "rs193921002",
      "frequency_reference_population": 0.0000061959404,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 10,
      "gnomad_exomes_af": 0.00000478883,
      "gnomad_genomes_af": 0.0000197075,
      "gnomad_exomes_ac": 7,
      "gnomad_genomes_ac": 3,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.4645960330963135,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.395,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.6579,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.03,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 5.9,
      "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": 2,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2",
      "acmg_by_gene": [
        {
          "score": 2,
          "benign_score": 0,
          "pathogenic_score": 2,
          "criteria": [
            "PM2"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000372310.8",
          "gene_symbol": "SLC6A9",
          "hgnc_id": 11056,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR,Unknown",
          "hgvs_c": "c.577G>A",
          "hgvs_p": "p.Glu193Lys"
        }
      ],
      "clinvar_disease": "Atypical glycine encephalopathy,Prostate cancer",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "Prostate cancer|Atypical glycine encephalopathy",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}