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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: 1-113834340-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=113834340&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 113834340,
      "ref": "A",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000359785.10",
      "consequences": [
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1994T>C",
          "hgvs_p": "p.Phe665Ser",
          "transcript": "ENST00000359785.10",
          "protein_id": "ENSP00000352833.5",
          "transcript_support_level": 1,
          "aa_start": 665,
          "aa_end": null,
          "aa_length": 807,
          "cds_start": 1994,
          "cds_end": null,
          "cds_length": 2424,
          "cdna_start": 2083,
          "cdna_end": null,
          "cdna_length": 3607,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1994T>C",
          "hgvs_p": "p.Phe665Ser",
          "transcript": "ENST00000420377.6",
          "protein_id": "ENSP00000388229.2",
          "transcript_support_level": 1,
          "aa_start": 665,
          "aa_end": null,
          "aa_length": 795,
          "cds_start": 1994,
          "cds_end": null,
          "cds_length": 2388,
          "cdna_start": 2083,
          "cdna_end": null,
          "cdna_length": 2726,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1922T>C",
          "hgvs_p": "p.Phe641Ser",
          "transcript": "ENST00000538253.5",
          "protein_id": "ENSP00000439372.2",
          "transcript_support_level": 1,
          "aa_start": 641,
          "aa_end": null,
          "aa_length": 783,
          "cds_start": 1922,
          "cds_end": null,
          "cds_length": 2352,
          "cdna_start": 2052,
          "cdna_end": null,
          "cdna_length": 3575,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1829T>C",
          "hgvs_p": "p.Phe610Ser",
          "transcript": "ENST00000528414.5",
          "protein_id": "ENSP00000435176.1",
          "transcript_support_level": 1,
          "aa_start": 610,
          "aa_end": null,
          "aa_length": 752,
          "cds_start": 1829,
          "cds_end": null,
          "cds_length": 2259,
          "cdna_start": 1904,
          "cdna_end": null,
          "cdna_length": 3424,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1613T>C",
          "hgvs_p": "p.Phe538Ser",
          "transcript": "ENST00000525799.1",
          "protein_id": "ENSP00000432674.1",
          "transcript_support_level": 1,
          "aa_start": 538,
          "aa_end": null,
          "aa_length": 668,
          "cds_start": 1613,
          "cds_end": null,
          "cds_length": 2007,
          "cdna_start": 1702,
          "cdna_end": null,
          "cdna_length": 2118,
          "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": 8,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.469-14686T>C",
          "hgvs_p": null,
          "transcript": "ENST00000460620.5",
          "protein_id": "ENSP00000433141.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 179,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 540,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1794,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1994T>C",
          "hgvs_p": "p.Phe665Ser",
          "transcript": "NM_015967.8",
          "protein_id": "NP_057051.4",
          "transcript_support_level": null,
          "aa_start": 665,
          "aa_end": null,
          "aa_length": 807,
          "cds_start": 1994,
          "cds_end": null,
          "cds_length": 2424,
          "cdna_start": 2083,
          "cdna_end": null,
          "cdna_length": 3607,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1922T>C",
          "hgvs_p": "p.Phe641Ser",
          "transcript": "NM_001308297.2",
          "protein_id": "NP_001295226.2",
          "transcript_support_level": null,
          "aa_start": 641,
          "aa_end": null,
          "aa_length": 783,
          "cds_start": 1922,
          "cds_end": null,
          "cds_length": 2352,
          "cdna_start": 2011,
          "cdna_end": null,
          "cdna_length": 3535,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1829T>C",
          "hgvs_p": "p.Phe610Ser",
          "transcript": "NM_012411.6",
          "protein_id": "NP_036543.5",
          "transcript_support_level": null,
          "aa_start": 610,
          "aa_end": null,
          "aa_length": 752,
          "cds_start": 1829,
          "cds_end": null,
          "cds_length": 2259,
          "cdna_start": 1918,
          "cdna_end": null,
          "cdna_length": 3442,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1916T>C",
          "hgvs_p": "p.Phe639Ser",
          "transcript": "XM_011541221.2",
          "protein_id": "XP_011539523.1",
          "transcript_support_level": null,
          "aa_start": 639,
          "aa_end": null,
          "aa_length": 781,
          "cds_start": 1916,
          "cds_end": null,
          "cds_length": 2346,
          "cdna_start": 2052,
          "cdna_end": null,
          "cdna_length": 3576,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1994T>C",
          "hgvs_p": "p.Phe665Ser",
          "transcript": "XM_011541222.2",
          "protein_id": "XP_011539524.1",
          "transcript_support_level": null,
          "aa_start": 665,
          "aa_end": null,
          "aa_length": 773,
          "cds_start": 1994,
          "cds_end": null,
          "cds_length": 2322,
          "cdna_start": 2130,
          "cdna_end": null,
          "cdna_length": 3623,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1844T>C",
          "hgvs_p": "p.Phe615Ser",
          "transcript": "XM_047417630.1",
          "protein_id": "XP_047273586.1",
          "transcript_support_level": null,
          "aa_start": 615,
          "aa_end": null,
          "aa_length": 757,
          "cds_start": 1844,
          "cds_end": null,
          "cds_length": 2274,
          "cdna_start": 1980,
          "cdna_end": null,
          "cdna_length": 3504,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1922T>C",
          "hgvs_p": "p.Phe641Ser",
          "transcript": "XM_011541225.3",
          "protein_id": "XP_011539527.1",
          "transcript_support_level": null,
          "aa_start": 641,
          "aa_end": null,
          "aa_length": 749,
          "cds_start": 1922,
          "cds_end": null,
          "cds_length": 2250,
          "cdna_start": 2058,
          "cdna_end": null,
          "cdna_length": 3551,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1994T>C",
          "hgvs_p": "p.Phe665Ser",
          "transcript": "XM_011541223.3",
          "protein_id": "XP_011539525.1",
          "transcript_support_level": null,
          "aa_start": 665,
          "aa_end": null,
          "aa_length": 715,
          "cds_start": 1994,
          "cds_end": null,
          "cds_length": 2148,
          "cdna_start": 2130,
          "cdna_end": null,
          "cdna_length": 3815,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "F",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1649T>C",
          "hgvs_p": "p.Phe550Ser",
          "transcript": "XM_017001005.3",
          "protein_id": "XP_016856494.1",
          "transcript_support_level": null,
          "aa_start": 550,
          "aa_end": null,
          "aa_length": 692,
          "cds_start": 1649,
          "cds_end": null,
          "cds_length": 2079,
          "cdna_start": 1987,
          "cdna_end": null,
          "cdna_length": 3511,
          "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": 15,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "n.2035T>C",
          "hgvs_p": null,
          "transcript": "ENST00000484147.5",
          "protein_id": null,
          "transcript_support_level": 2,
          "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": 2258,
          "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": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "n.*1272T>C",
          "hgvs_p": null,
          "transcript": "ENST00000532224.5",
          "protein_id": "ENSP00000431249.1",
          "transcript_support_level": 2,
          "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": 2421,
          "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": 11,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "n.*1272T>C",
          "hgvs_p": null,
          "transcript": "ENST00000532224.5",
          "protein_id": "ENSP00000431249.1",
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 2421,
          "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": 21,
          "intron_rank": 15,
          "intron_rank_end": null,
          "gene_symbol": "PTPN22",
          "gene_hgnc_id": 9652,
          "hgvs_c": "c.1941+53T>C",
          "hgvs_p": null,
          "transcript": "NM_001193431.3",
          "protein_id": "NP_001180360.2",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": 779,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2340,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3523,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": 4,
          "intron_rank_end": null,
          "gene_symbol": "AP4B1-AS1",
          "gene_hgnc_id": 44114,
          "hgvs_c": "n.470+2527A>G",
          "hgvs_p": null,
          "transcript": "ENST00000664434.1",
          "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": 802,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "AP4B1-AS1",
          "gene_hgnc_id": 44114,
          "hgvs_c": "n.440+18868A>G",
          "hgvs_p": null,
          "transcript": "ENST00000717022.1",
          "protein_id": null,
          "transcript_support_level": null,
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        {
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        {
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        },
        {
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          ],
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          "exon_count": 20,
          "intron_rank": 14,
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          "gene_symbol": "PTPN22",
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          "hgvs_c": "c.1869+53T>C",
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          "transcript": "XM_047417631.1",
          "protein_id": "XP_047273587.1",
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        },
        {
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          ],
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          "gene_symbol": "PTPN22",
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          "hgvs_c": "c.1863+53T>C",
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          "transcript": "XM_047417632.1",
          "protein_id": "XP_047273588.1",
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          "cds_start": -4,
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          "cdna_start": null,
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          "cdna_length": 3492,
          "mane_select": null,
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        }
      ],
      "gene_symbol": "PTPN22",
      "gene_hgnc_id": 9652,
      "dbsnp": "rs776367870",
      "frequency_reference_population": 0.000021684878,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 35,
      "gnomad_exomes_af": 0.0000212076,
      "gnomad_genomes_af": 0.000026266,
      "gnomad_exomes_ac": 31,
      "gnomad_genomes_ac": 4,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.011924535036087036,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.018,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0651,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.71,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -1.276,
      "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": -6,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4_Strong,BP6_Moderate",
      "acmg_by_gene": [
        {
          "score": -6,
          "benign_score": 6,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Moderate"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000359785.10",
          "gene_symbol": "PTPN22",
          "hgnc_id": 9652,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "Unknown,AR",
          "hgvs_c": "c.1994T>C",
          "hgvs_p": "p.Phe665Ser"
        },
        {
          "score": -6,
          "benign_score": 6,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Moderate"
          ],
          "verdict": "Likely_benign",
          "transcript": "NR_125965.1",
          "gene_symbol": "AP4B1-AS1",
          "hgnc_id": 44114,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.414+18868A>G",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "not specified",
      "clinvar_classification": "Likely benign",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "LB:1",
      "phenotype_combined": "not specified",
      "pathogenicity_classification_combined": "Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}