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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: 11-116849197-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=116849197&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "11",
      "pos": 116849197,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_001366686.3",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3742C>T",
          "hgvs_p": "p.Arg1248Cys",
          "transcript": "NM_001366686.3",
          "protein_id": "NP_001353615.1",
          "transcript_support_level": null,
          "aa_start": 1248,
          "aa_end": null,
          "aa_length": 1369,
          "cds_start": 3742,
          "cds_end": null,
          "cds_length": 4110,
          "cdna_start": 3755,
          "cdna_end": null,
          "cdna_length": 6364,
          "mane_select": "ENST00000445177.6",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3742C>T",
          "hgvs_p": "p.Arg1248Cys",
          "transcript": "ENST00000445177.6",
          "protein_id": "ENSP00000391295.2",
          "transcript_support_level": 5,
          "aa_start": 1248,
          "aa_end": null,
          "aa_length": 1369,
          "cds_start": 3742,
          "cds_end": null,
          "cds_length": 4110,
          "cdna_start": 3755,
          "cdna_end": null,
          "cdna_length": 6364,
          "mane_select": "NM_001366686.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3418C>T",
          "hgvs_p": "p.Arg1140Cys",
          "transcript": "ENST00000446921.6",
          "protein_id": "ENSP00000390442.2",
          "transcript_support_level": 1,
          "aa_start": 1140,
          "aa_end": null,
          "aa_length": 1261,
          "cds_start": 3418,
          "cds_end": null,
          "cds_length": 3786,
          "cdna_start": 3440,
          "cdna_end": null,
          "cdna_length": 3858,
          "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": 22,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "n.*2942C>T",
          "hgvs_p": null,
          "transcript": "ENST00000415541.5",
          "protein_id": "ENSP00000392761.1",
          "transcript_support_level": 1,
          "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": 3816,
          "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": 7,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "n.1611C>T",
          "hgvs_p": null,
          "transcript": "ENST00000488337.5",
          "protein_id": null,
          "transcript_support_level": 1,
          "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": 4220,
          "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": 22,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "n.*2942C>T",
          "hgvs_p": null,
          "transcript": "ENST00000415541.5",
          "protein_id": "ENSP00000392761.1",
          "transcript_support_level": 1,
          "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": 3816,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3598C>T",
          "hgvs_p": "p.Arg1200Cys",
          "transcript": "NM_025164.6",
          "protein_id": "NP_079440.3",
          "transcript_support_level": null,
          "aa_start": 1200,
          "aa_end": null,
          "aa_length": 1321,
          "cds_start": 3598,
          "cds_end": null,
          "cds_length": 3966,
          "cdna_start": 3611,
          "cdna_end": null,
          "cdna_length": 6212,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3598C>T",
          "hgvs_p": "p.Arg1200Cys",
          "transcript": "ENST00000375300.6",
          "protein_id": "ENSP00000364449.1",
          "transcript_support_level": 2,
          "aa_start": 1200,
          "aa_end": null,
          "aa_length": 1321,
          "cds_start": 3598,
          "cds_end": null,
          "cds_length": 3966,
          "cdna_start": 3611,
          "cdna_end": null,
          "cdna_length": 6207,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3418C>T",
          "hgvs_p": "p.Arg1140Cys",
          "transcript": "NM_001281749.3",
          "protein_id": "NP_001268678.1",
          "transcript_support_level": null,
          "aa_start": 1140,
          "aa_end": null,
          "aa_length": 1261,
          "cds_start": 3418,
          "cds_end": null,
          "cds_length": 3786,
          "cdna_start": 3431,
          "cdna_end": null,
          "cdna_length": 6032,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.2941C>T",
          "hgvs_p": "p.Arg981Cys",
          "transcript": "NM_001281748.3",
          "protein_id": "NP_001268677.1",
          "transcript_support_level": null,
          "aa_start": 981,
          "aa_end": null,
          "aa_length": 1102,
          "cds_start": 2941,
          "cds_end": null,
          "cds_length": 3309,
          "cdna_start": 3555,
          "cdna_end": null,
          "cdna_length": 6156,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
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          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3742C>T",
          "hgvs_p": "p.Arg1248Cys",
          "transcript": "XM_047426671.1",
          "protein_id": "XP_047282627.1",
          "transcript_support_level": null,
          "aa_start": 1248,
          "aa_end": null,
          "aa_length": 1369,
          "cds_start": 3742,
          "cds_end": null,
          "cds_length": 4110,
          "cdna_start": 3755,
          "cdna_end": null,
          "cdna_length": 4142,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
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          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3598C>T",
          "hgvs_p": "p.Arg1200Cys",
          "transcript": "XM_005271482.5",
          "protein_id": "XP_005271539.2",
          "transcript_support_level": null,
          "aa_start": 1200,
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          "cds_start": 3598,
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          "cds_length": 3966,
          "cdna_start": 3611,
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          "cdna_length": 6220,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
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        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
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          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3562C>T",
          "hgvs_p": "p.Arg1188Cys",
          "transcript": "XM_011542722.2",
          "protein_id": "XP_011541024.1",
          "transcript_support_level": null,
          "aa_start": 1188,
          "aa_end": null,
          "aa_length": 1309,
          "cds_start": 3562,
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          "cdna_start": 3575,
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          "cdna_length": 6184,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3454C>T",
          "hgvs_p": "p.Arg1152Cys",
          "transcript": "XM_047426672.1",
          "protein_id": "XP_047282628.1",
          "transcript_support_level": null,
          "aa_start": 1152,
          "aa_end": null,
          "aa_length": 1273,
          "cds_start": 3454,
          "cds_end": null,
          "cds_length": 3822,
          "cdna_start": 3467,
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          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
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          "intron_rank": null,
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          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3418C>T",
          "hgvs_p": "p.Arg1140Cys",
          "transcript": "XM_005271484.4",
          "protein_id": "XP_005271541.2",
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          "aa_length": 1261,
          "cds_start": 3418,
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          "cdna_start": 3431,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3274C>T",
          "hgvs_p": "p.Arg1092Cys",
          "transcript": "XM_017017424.2",
          "protein_id": "XP_016872913.1",
          "transcript_support_level": null,
          "aa_start": 1092,
          "aa_end": null,
          "aa_length": 1213,
          "cds_start": 3274,
          "cds_end": null,
          "cds_length": 3642,
          "cdna_start": 3287,
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          "mane_select": null,
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          "biotype": null,
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        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3265C>T",
          "hgvs_p": "p.Arg1089Cys",
          "transcript": "XM_011542723.3",
          "protein_id": "XP_011541025.1",
          "transcript_support_level": null,
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          "aa_end": null,
          "aa_length": 1210,
          "cds_start": 3265,
          "cds_end": null,
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          "cdna_start": 3628,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 21,
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          "exon_count": 24,
          "intron_rank": null,
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          "gene_symbol": "SIK3",
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          "hgvs_c": "c.3265C>T",
          "hgvs_p": "p.Arg1089Cys",
          "transcript": "XM_011542724.3",
          "protein_id": "XP_011541026.1",
          "transcript_support_level": null,
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        },
        {
          "aa_ref": "R",
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          "strand": false,
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          ],
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          "intron_rank": null,
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          "gene_symbol": "SIK3",
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          "hgvs_c": "c.3265C>T",
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          "transcript": "XM_011542725.3",
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          "biotype": null,
          "feature": null
        },
        {
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          "strand": false,
          "consequences": [
            "missense_variant"
          ],
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          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SIK3",
          "gene_hgnc_id": 29165,
          "hgvs_c": "c.3265C>T",
          "hgvs_p": "p.Arg1089Cys",
          "transcript": "XM_017017425.2",
          "protein_id": "XP_016872914.1",
          "transcript_support_level": null,
          "aa_start": 1089,
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          "cds_start": 3265,
          "cds_end": null,
          "cds_length": 3633,
          "cdna_start": 6767,
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          "cdna_length": 9376,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 23,
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        {
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      ],
      "gene_symbol": "SIK3",
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      "dbsnp": "rs747877301",
      "frequency_reference_population": 0.000019153655,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 28,
      "gnomad_exomes_af": 0.0000191537,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 28,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.49198153614997864,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.05000000074505806,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.211,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0881,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.16,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 3.136,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.05,
      "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": 0,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "",
      "acmg_by_gene": [
        {
          "score": 0,
          "benign_score": 0,
          "pathogenic_score": 0,
          "criteria": [],
          "verdict": "Uncertain_significance",
          "transcript": "NM_001366686.3",
          "gene_symbol": "SIK3",
          "hgnc_id": 29165,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR,AD,Unknown",
          "hgvs_c": "c.3742C>T",
          "hgvs_p": "p.Arg1248Cys"
        },
        {
          "score": 0,
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          "pathogenic_score": 0,
          "criteria": [],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000444200.2",
          "gene_symbol": "APOA1-AS",
          "hgnc_id": 40079,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.124-6093G>A",
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      ],
      "clinvar_disease": "not specified",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "not specified",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}