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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: 16-786368-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=786368&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "16",
      "pos": 786368,
      "ref": "T",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "NM_001324086.2",
      "consequences": [
        {
          "aa_ref": "H",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.521A>G",
          "hgvs_p": "p.His174Arg",
          "transcript": "NM_058192.3",
          "protein_id": "NP_478072.1",
          "transcript_support_level": null,
          "aa_start": 174,
          "aa_end": null,
          "aa_length": 312,
          "cds_start": 521,
          "cds_end": null,
          "cds_length": 939,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000007264.7",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_058192.3"
        },
        {
          "aa_ref": "H",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.521A>G",
          "hgvs_p": "p.His174Arg",
          "transcript": "ENST00000007264.7",
          "protein_id": "ENSP00000007264.2",
          "transcript_support_level": 2,
          "aa_start": 174,
          "aa_end": null,
          "aa_length": 312,
          "cds_start": 521,
          "cds_end": null,
          "cds_length": 939,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_058192.3",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000007264.7"
        },
        {
          "aa_ref": "H",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.521A>G",
          "hgvs_p": "p.His174Arg",
          "transcript": "ENST00000561734.5",
          "protein_id": "ENSP00000455026.1",
          "transcript_support_level": 1,
          "aa_start": 174,
          "aa_end": null,
          "aa_length": 312,
          "cds_start": 521,
          "cds_end": null,
          "cds_length": 939,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000561734.5"
        },
        {
          "aa_ref": "H",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.530A>G",
          "hgvs_p": "p.His177Arg",
          "transcript": "NM_001324086.2",
          "protein_id": "NP_001311015.1",
          "transcript_support_level": null,
          "aa_start": 177,
          "aa_end": null,
          "aa_length": 315,
          "cds_start": 530,
          "cds_end": null,
          "cds_length": 948,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001324086.2"
        },
        {
          "aa_ref": "H",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.521A>G",
          "hgvs_p": "p.His174Arg",
          "transcript": "ENST00000918138.1",
          "protein_id": "ENSP00000588197.1",
          "transcript_support_level": null,
          "aa_start": 174,
          "aa_end": null,
          "aa_length": 312,
          "cds_start": 521,
          "cds_end": null,
          "cds_length": 939,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000918138.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.473A>G",
          "hgvs_p": "p.His158Arg",
          "transcript": "NM_001369658.1",
          "protein_id": "NP_001356587.1",
          "transcript_support_level": null,
          "aa_start": 158,
          "aa_end": null,
          "aa_length": 296,
          "cds_start": 473,
          "cds_end": null,
          "cds_length": 891,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001369658.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.428A>G",
          "hgvs_p": "p.His143Arg",
          "transcript": "ENST00000947984.1",
          "protein_id": "ENSP00000618043.1",
          "transcript_support_level": null,
          "aa_start": 143,
          "aa_end": null,
          "aa_length": 281,
          "cds_start": 428,
          "cds_end": null,
          "cds_length": 846,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000947984.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.419A>G",
          "hgvs_p": "p.His140Arg",
          "transcript": "ENST00000918139.1",
          "protein_id": "ENSP00000588198.1",
          "transcript_support_level": null,
          "aa_start": 140,
          "aa_end": null,
          "aa_length": 278,
          "cds_start": 419,
          "cds_end": null,
          "cds_length": 837,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000918139.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.419A>G",
          "hgvs_p": "p.His140Arg",
          "transcript": "ENST00000947985.1",
          "protein_id": "ENSP00000618044.1",
          "transcript_support_level": null,
          "aa_start": 140,
          "aa_end": null,
          "aa_length": 278,
          "cds_start": 419,
          "cds_end": null,
          "cds_length": 837,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000947985.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.143A>G",
          "hgvs_p": "p.His48Arg",
          "transcript": "NM_001324410.2",
          "protein_id": "NP_001311339.1",
          "transcript_support_level": null,
          "aa_start": 48,
          "aa_end": null,
          "aa_length": 186,
          "cds_start": 143,
          "cds_end": null,
          "cds_length": 561,
          "cdna_start": null,
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          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001324410.2"
        },
        {
          "aa_ref": "H",
          "aa_alt": "R",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.143A>G",
          "hgvs_p": "p.His48Arg",
          "transcript": "NM_001369659.1",
          "protein_id": "NP_001356588.1",
          "transcript_support_level": null,
          "aa_start": 48,
          "aa_end": null,
          "aa_length": 186,
          "cds_start": 143,
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          "cds_length": 561,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001369659.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": "R",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
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          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.134A>G",
          "hgvs_p": "p.His45Arg",
          "transcript": "NM_001324412.2",
          "protein_id": "NP_001311341.1",
          "transcript_support_level": null,
          "aa_start": 45,
          "aa_end": null,
          "aa_length": 183,
          "cds_start": 134,
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          "cds_length": 552,
          "cdna_start": null,
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          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001324412.2"
        },
        {
          "aa_ref": "H",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 6,
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          "exon_count": 6,
          "intron_rank": null,
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          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.134A>G",
          "hgvs_p": "p.His45Arg",
          "transcript": "NM_001324413.2",
          "protein_id": "NP_001311342.1",
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          "cds_start": 134,
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          "cdna_start": null,
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          "biotype": "protein_coding",
          "feature": "NM_001324413.2"
        },
        {
          "aa_ref": "H",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.134A>G",
          "hgvs_p": "p.His45Arg",
          "transcript": "NM_001324414.2",
          "protein_id": "NP_001311343.1",
          "transcript_support_level": null,
          "aa_start": 45,
          "aa_end": null,
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          "cds_start": 134,
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          "cds_length": 552,
          "cdna_start": null,
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        {
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          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.134A>G",
          "hgvs_p": "p.His45Arg",
          "transcript": "NM_001324415.2",
          "protein_id": "NP_001311344.1",
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          "cds_start": 134,
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          "biotype": "protein_coding",
          "feature": "NM_001324415.2"
        },
        {
          "aa_ref": "H",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 6,
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          "exon_count": 6,
          "intron_rank": null,
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          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.134A>G",
          "hgvs_p": "p.His45Arg",
          "transcript": "NM_001369660.1",
          "protein_id": "NP_001356589.1",
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          "cds_start": 134,
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          "cdna_start": null,
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          "biotype": "protein_coding",
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        {
          "aa_ref": "H",
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          "strand": false,
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          ],
          "exon_rank": 5,
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          "intron_rank": null,
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          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.134A>G",
          "hgvs_p": "p.His45Arg",
          "transcript": "ENST00000567114.5",
          "protein_id": "ENSP00000455862.1",
          "transcript_support_level": 2,
          "aa_start": 45,
          "aa_end": null,
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        {
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          "intron_rank": null,
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          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.143A>G",
          "hgvs_p": "p.His48Arg",
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        {
          "aa_ref": "H",
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          ],
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          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.134A>G",
          "hgvs_p": "p.His45Arg",
          "transcript": "ENST00000565377.1",
          "protein_id": "ENSP00000456692.1",
          "transcript_support_level": 2,
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        },
        {
          "aa_ref": null,
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          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.*244A>G",
          "hgvs_p": null,
          "transcript": "ENST00000562070.1",
          "protein_id": "ENSP00000458059.1",
          "transcript_support_level": 2,
          "aa_start": null,
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          "aa_length": 177,
          "cds_start": null,
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          "cds_length": 534,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": null,
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          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.*22A>G",
          "hgvs_p": null,
          "transcript": "NM_001324411.2",
          "protein_id": "NP_001311340.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 131,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 396,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001324411.2"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "c.*22A>G",
          "hgvs_p": null,
          "transcript": "ENST00000565809.5",
          "protein_id": "ENSP00000457722.1",
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 131,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 396,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000565809.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "n.*105A>G",
          "hgvs_p": null,
          "transcript": "ENST00000567283.5",
          "protein_id": "ENSP00000457527.1",
          "transcript_support_level": 3,
          "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": "ENST00000567283.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPUSD1",
          "gene_hgnc_id": 14173,
          "hgvs_c": "n.*105A>G",
          "hgvs_p": null,
          "transcript": "ENST00000567283.5",
          "protein_id": "ENSP00000457527.1",
          "transcript_support_level": 3,
          "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": "ENST00000567283.5"
        }
      ],
      "gene_symbol": "RPUSD1",
      "gene_hgnc_id": 14173,
      "dbsnp": "rs193920771",
      "frequency_reference_population": null,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 0,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.9839049577713013,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.701,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9868,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.18,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 6.112,
      "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": 6,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PM2,PP3_Strong",
      "acmg_by_gene": [
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PM2",
            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "NM_001324086.2",
          "gene_symbol": "RPUSD1",
          "hgnc_id": 14173,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.530A>G",
          "hgvs_p": "p.His177Arg"
        }
      ],
      "clinvar_disease": "Prostate cancer",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "no assertion criteria provided",
      "clinvar_submissions_summary": "null",
      "phenotype_combined": "Prostate cancer",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}