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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: 3-11025564-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=11025564&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 11025564,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_003042.4",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "NM_003042.4",
          "protein_id": "NP_003033.3",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000287766.10",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_003042.4"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000287766.10",
          "protein_id": "ENSP00000287766.4",
          "transcript_support_level": 1,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_003042.4",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000287766.10"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.902G>A",
          "hgvs_p": "p.Arg301His",
          "transcript": "ENST00000698198.1",
          "protein_id": "ENSP00000513602.1",
          "transcript_support_level": null,
          "aa_start": 301,
          "aa_end": null,
          "aa_length": 623,
          "cds_start": 902,
          "cds_end": null,
          "cds_length": 1872,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000698198.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000644803.1",
          "protein_id": "ENSP00000494469.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 608,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1827,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000644803.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "NM_001348250.2",
          "protein_id": "NP_001335179.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001348250.2"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000642201.1",
          "protein_id": "ENSP00000494778.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000642201.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000642515.1",
          "protein_id": "ENSP00000496348.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000642515.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000642639.1",
          "protein_id": "ENSP00000494191.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000642639.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000642735.1",
          "protein_id": "ENSP00000494050.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000642735.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000642767.1",
          "protein_id": "ENSP00000494346.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000642767.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000642820.1",
          "protein_id": "ENSP00000495900.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000642820.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000643396.1",
          "protein_id": "ENSP00000494136.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000643396.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000643498.1",
          "protein_id": "ENSP00000494997.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000643498.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000645029.1",
          "protein_id": "ENSP00000496171.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000645029.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000645054.1",
          "protein_id": "ENSP00000495751.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000645054.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000645592.1",
          "protein_id": "ENSP00000496619.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000645592.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000645974.1",
          "protein_id": "ENSP00000496390.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000645974.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000646022.1",
          "protein_id": "ENSP00000494134.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000646022.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000646060.1",
          "protein_id": "ENSP00000496302.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000646060.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SLC6A1",
          "gene_hgnc_id": 11042,
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His",
          "transcript": "ENST00000646570.1",
          "protein_id": "ENSP00000496064.1",
          "transcript_support_level": null,
          "aa_start": 277,
          "aa_end": null,
          "aa_length": 599,
          "cds_start": 830,
          "cds_end": null,
          "cds_length": 1800,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
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          "consequences": [
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          "transcript": "ENST00000643326.1",
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        {
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          "exon_count": 14,
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        {
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          "protein_coding": true,
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          "consequences": [
            "downstream_gene_variant"
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          "exon_count": 8,
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          "gene_symbol": "SLC6A1",
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          "hgvs_c": "c.*94G>A",
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          "transcript": "ENST00000425938.6",
          "protein_id": "ENSP00000411689.2",
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          "cds_length": 376,
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          "biotype": "protein_coding",
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        },
        {
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          "consequences": [
            "downstream_gene_variant"
          ],
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          "exon_count": 9,
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          "gene_symbol": "SLC6A1",
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          "hgvs_c": "n.*403G>A",
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          "transcript": "ENST00000460480.2",
          "protein_id": "ENSP00000494289.1",
          "transcript_support_level": 4,
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          "cdna_start": null,
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          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000460480.2"
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      ],
      "gene_symbol": "SLC6A1",
      "gene_hgnc_id": 11042,
      "dbsnp": "rs752396911",
      "frequency_reference_population": 0.00002850129,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 46,
      "gnomad_exomes_af": 0.0000266809,
      "gnomad_genomes_af": 0.0000459794,
      "gnomad_exomes_ac": 39,
      "gnomad_genomes_ac": 7,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.2239978015422821,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.196,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0776,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.41,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 2.142,
      "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": -5,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "PM1,BP4_Moderate,BP6,BS2",
      "acmg_by_gene": [
        {
          "score": -5,
          "benign_score": 7,
          "pathogenic_score": 2,
          "criteria": [
            "PM1",
            "BP4_Moderate",
            "BP6",
            "BS2"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_003042.4",
          "gene_symbol": "SLC6A1",
          "hgnc_id": 11042,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,Unknown",
          "hgvs_c": "c.830G>A",
          "hgvs_p": "p.Arg277His"
        }
      ],
      "clinvar_disease": "Epilepsy with myoclonic atonic seizures,Self-limited epilepsy with centrotemporal spikes,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:3 B:1",
      "phenotype_combined": "Self-limited epilepsy with centrotemporal spikes|not specified|Epilepsy with myoclonic atonic seizures",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}