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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: 16-2086268-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2086268&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "16",
      "pos": 2086268,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "NM_000548.5",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4738C>T",
          "hgvs_p": "p.Arg1580Trp",
          "transcript": "NM_000548.5",
          "protein_id": "NP_000539.2",
          "transcript_support_level": null,
          "aa_start": 1580,
          "aa_end": null,
          "aa_length": 1807,
          "cds_start": 4738,
          "cds_end": null,
          "cds_length": 5424,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000219476.9",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_000548.5"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4738C>T",
          "hgvs_p": "p.Arg1580Trp",
          "transcript": "ENST00000219476.9",
          "protein_id": "ENSP00000219476.3",
          "transcript_support_level": 5,
          "aa_start": 1580,
          "aa_end": null,
          "aa_length": 1807,
          "cds_start": 4738,
          "cds_end": null,
          "cds_length": 5424,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_000548.5",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000219476.9"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4669C>T",
          "hgvs_p": "p.Arg1557Trp",
          "transcript": "ENST00000350773.9",
          "protein_id": "ENSP00000344383.4",
          "transcript_support_level": 1,
          "aa_start": 1557,
          "aa_end": null,
          "aa_length": 1784,
          "cds_start": 4669,
          "cds_end": null,
          "cds_length": 5355,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000350773.9"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 35,
          "exon_rank_end": null,
          "exon_count": 40,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4537C>T",
          "hgvs_p": "p.Arg1513Trp",
          "transcript": "ENST00000401874.7",
          "protein_id": "ENSP00000384468.2",
          "transcript_support_level": 1,
          "aa_start": 1513,
          "aa_end": null,
          "aa_length": 1740,
          "cds_start": 4537,
          "cds_end": null,
          "cds_length": 5223,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000401874.7"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 33,
          "exon_rank_end": null,
          "exon_count": 38,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "n.*3905C>T",
          "hgvs_p": null,
          "transcript": "ENST00000439117.6",
          "protein_id": "ENSP00000406980.2",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000439117.6"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 33,
          "exon_rank_end": null,
          "exon_count": 38,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "n.*3905C>T",
          "hgvs_p": null,
          "transcript": "ENST00000439117.6",
          "protein_id": "ENSP00000406980.2",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000439117.6"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4828C>T",
          "hgvs_p": "p.Arg1610Trp",
          "transcript": "ENST00000645186.2",
          "protein_id": "ENSP00000495110.2",
          "transcript_support_level": null,
          "aa_start": 1610,
          "aa_end": null,
          "aa_length": 1837,
          "cds_start": 4828,
          "cds_end": null,
          "cds_length": 5514,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000645186.2"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4735C>T",
          "hgvs_p": "p.Arg1579Trp",
          "transcript": "NM_001406663.1",
          "protein_id": "NP_001393592.1",
          "transcript_support_level": null,
          "aa_start": 1579,
          "aa_end": null,
          "aa_length": 1806,
          "cds_start": 4735,
          "cds_end": null,
          "cds_length": 5421,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001406663.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4735C>T",
          "hgvs_p": "p.Arg1579Trp",
          "transcript": "ENST00000642365.2",
          "protein_id": "ENSP00000495459.2",
          "transcript_support_level": null,
          "aa_start": 1579,
          "aa_end": null,
          "aa_length": 1806,
          "cds_start": 4735,
          "cds_end": null,
          "cds_length": 5421,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000642365.2"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4732C>T",
          "hgvs_p": "p.Arg1578Trp",
          "transcript": "ENST00000646388.1",
          "protein_id": "ENSP00000495921.1",
          "transcript_support_level": null,
          "aa_start": 1578,
          "aa_end": null,
          "aa_length": 1805,
          "cds_start": 4732,
          "cds_end": null,
          "cds_length": 5418,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000646388.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4714C>T",
          "hgvs_p": "p.Arg1572Trp",
          "transcript": "ENST00000941763.1",
          "protein_id": "ENSP00000611822.1",
          "transcript_support_level": null,
          "aa_start": 1572,
          "aa_end": null,
          "aa_length": 1799,
          "cds_start": 4714,
          "cds_end": null,
          "cds_length": 5400,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000941763.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4705C>T",
          "hgvs_p": "p.Arg1569Trp",
          "transcript": "ENST00000903285.1",
          "protein_id": "ENSP00000573344.1",
          "transcript_support_level": null,
          "aa_start": 1569,
          "aa_end": null,
          "aa_length": 1796,
          "cds_start": 4705,
          "cds_end": null,
          "cds_length": 5391,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000903285.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4669C>T",
          "hgvs_p": "p.Arg1557Trp",
          "transcript": "NM_001114382.3",
          "protein_id": "NP_001107854.1",
          "transcript_support_level": null,
          "aa_start": 1557,
          "aa_end": null,
          "aa_length": 1784,
          "cds_start": 4669,
          "cds_end": null,
          "cds_length": 5355,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001114382.3"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4666C>T",
          "hgvs_p": "p.Arg1556Trp",
          "transcript": "NM_001406664.1",
          "protein_id": "NP_001393593.1",
          "transcript_support_level": null,
          "aa_start": 1556,
          "aa_end": null,
          "aa_length": 1783,
          "cds_start": 4666,
          "cds_end": null,
          "cds_length": 5352,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001406664.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4663C>T",
          "hgvs_p": "p.Arg1555Trp",
          "transcript": "ENST00000643946.1",
          "protein_id": "ENSP00000495927.1",
          "transcript_support_level": null,
          "aa_start": 1555,
          "aa_end": null,
          "aa_length": 1782,
          "cds_start": 4663,
          "cds_end": null,
          "cds_length": 5349,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000643946.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4660C>T",
          "hgvs_p": "p.Arg1554Trp",
          "transcript": "NM_001406665.1",
          "protein_id": "NP_001393594.1",
          "transcript_support_level": null,
          "aa_start": 1554,
          "aa_end": null,
          "aa_length": 1781,
          "cds_start": 4660,
          "cds_end": null,
          "cds_length": 5346,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001406665.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4660C>T",
          "hgvs_p": "p.Arg1554Trp",
          "transcript": "ENST00000941766.1",
          "protein_id": "ENSP00000611825.1",
          "transcript_support_level": null,
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          "aa_end": null,
          "aa_length": 1781,
          "cds_start": 4660,
          "cds_end": null,
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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": "ENST00000941766.1"
        },
        {
          "aa_ref": "R",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 35,
          "exon_rank_end": null,
          "exon_count": 40,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4657C>T",
          "hgvs_p": "p.Arg1553Trp",
          "transcript": "ENST00000644399.1",
          "protein_id": "ENSP00000493990.1",
          "transcript_support_level": null,
          "aa_start": 1553,
          "aa_end": null,
          "aa_length": 1780,
          "cds_start": 4657,
          "cds_end": null,
          "cds_length": 5343,
          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4657C>T",
          "hgvs_p": "p.Arg1553Trp",
          "transcript": "ENST00000903287.1",
          "protein_id": "ENSP00000573346.1",
          "transcript_support_level": null,
          "aa_start": 1553,
          "aa_end": null,
          "aa_length": 1780,
          "cds_start": 4657,
          "cds_end": null,
          "cds_length": 5343,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000903287.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 35,
          "exon_rank_end": null,
          "exon_count": 40,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4630C>T",
          "hgvs_p": "p.Arg1544Trp",
          "transcript": "NM_001406667.1",
          "protein_id": "NP_001393596.1",
          "transcript_support_level": null,
          "aa_start": 1544,
          "aa_end": null,
          "aa_length": 1771,
          "cds_start": 4630,
          "cds_end": null,
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        {
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        {
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          "transcript": "ENST00000644417.2",
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          "cdna_start": null,
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        {
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          "transcript": "ENST00000646464.2",
          "protein_id": "ENSP00000496610.2",
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          "cdna_start": null,
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          "biotype": "nonsense_mediated_decay",
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        },
        {
          "aa_ref": null,
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
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          "exon_count": 2,
          "intron_rank": null,
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          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "n.-102C>T",
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          "transcript": "ENST00000646557.1",
          "protein_id": null,
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          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
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          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000646557.1"
        }
      ],
      "gene_symbol": "TSC2",
      "gene_hgnc_id": 12363,
      "dbsnp": "rs777592623",
      "frequency_reference_population": 0.000013141641,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 2,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": 0.0000131416,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": 2,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.541889488697052,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.602,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.2855,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.11,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 4.036,
      "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": "PM1,PM2,BP6",
      "acmg_by_gene": [
        {
          "score": 3,
          "benign_score": 1,
          "pathogenic_score": 4,
          "criteria": [
            "PM1",
            "PM2",
            "BP6"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_000548.5",
          "gene_symbol": "TSC2",
          "hgnc_id": 12363,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.4738C>T",
          "hgvs_p": "p.Arg1580Trp"
        }
      ],
      "clinvar_disease": "Hereditary cancer-predisposing syndrome,Isolated focal cortical dysplasia type II,Tuberous sclerosis 2,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:3 LB:2",
      "phenotype_combined": "not provided|Tuberous sclerosis 2|Isolated focal cortical dysplasia type II|Hereditary cancer-predisposing syndrome",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}