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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: 15-89690616-C-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=89690616&ref=C&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "15",
      "pos": 89690616,
      "ref": "C",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "ENST00000300056.8",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX11A",
          "gene_hgnc_id": 8852,
          "hgvs_c": "c.17G>T",
          "hgvs_p": "p.Arg6Leu",
          "transcript": "NM_003847.3",
          "protein_id": "NP_003838.1",
          "transcript_support_level": null,
          "aa_start": 6,
          "aa_end": null,
          "aa_length": 247,
          "cds_start": 17,
          "cds_end": null,
          "cds_length": 744,
          "cdna_start": 139,
          "cdna_end": null,
          "cdna_length": 2708,
          "mane_select": "ENST00000300056.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "L",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX11A",
          "gene_hgnc_id": 8852,
          "hgvs_c": "c.17G>T",
          "hgvs_p": "p.Arg6Leu",
          "transcript": "ENST00000300056.8",
          "protein_id": "ENSP00000300056.3",
          "transcript_support_level": 1,
          "aa_start": 6,
          "aa_end": null,
          "aa_length": 247,
          "cds_start": 17,
          "cds_end": null,
          "cds_length": 744,
          "cdna_start": 139,
          "cdna_end": null,
          "cdna_length": 2708,
          "mane_select": "NM_003847.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX11A",
          "gene_hgnc_id": 8852,
          "hgvs_c": "c.17G>T",
          "hgvs_p": "p.Arg6Leu",
          "transcript": "NM_001271572.2",
          "protein_id": "NP_001258501.1",
          "transcript_support_level": null,
          "aa_start": 6,
          "aa_end": null,
          "aa_length": 216,
          "cds_start": 17,
          "cds_end": null,
          "cds_length": 651,
          "cdna_start": 139,
          "cdna_end": null,
          "cdna_length": 2615,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX11A",
          "gene_hgnc_id": 8852,
          "hgvs_c": "c.17G>T",
          "hgvs_p": "p.Arg6Leu",
          "transcript": "ENST00000561257.1",
          "protein_id": "ENSP00000453492.1",
          "transcript_support_level": 2,
          "aa_start": 6,
          "aa_end": null,
          "aa_length": 216,
          "cds_start": 17,
          "cds_end": null,
          "cds_length": 651,
          "cdna_start": 47,
          "cdna_end": null,
          "cdna_length": 978,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX11A",
          "gene_hgnc_id": 8852,
          "hgvs_c": "c.17G>T",
          "hgvs_p": "p.Arg6Leu",
          "transcript": "ENST00000561224.5",
          "protein_id": "ENSP00000453552.1",
          "transcript_support_level": 4,
          "aa_start": 6,
          "aa_end": null,
          "aa_length": 64,
          "cds_start": 17,
          "cds_end": null,
          "cds_length": 195,
          "cdna_start": 138,
          "cdna_end": null,
          "cdna_length": 529,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX11A",
          "gene_hgnc_id": 8852,
          "hgvs_c": "c.17G>T",
          "hgvs_p": "p.Arg6Leu",
          "transcript": "ENST00000559170.1",
          "protein_id": "ENSP00000453878.1",
          "transcript_support_level": 2,
          "aa_start": 6,
          "aa_end": null,
          "aa_length": 32,
          "cds_start": 17,
          "cds_end": null,
          "cds_length": 99,
          "cdna_start": 168,
          "cdna_end": null,
          "cdna_length": 905,
          "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": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX11A",
          "gene_hgnc_id": 8852,
          "hgvs_c": "n.167G>T",
          "hgvs_p": null,
          "transcript": "ENST00000557982.1",
          "protein_id": null,
          "transcript_support_level": 5,
          "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": 646,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "5_prime_UTR_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX11A",
          "gene_hgnc_id": 8852,
          "hgvs_c": "c.-303G>T",
          "hgvs_p": null,
          "transcript": "NM_001271573.2",
          "protein_id": "NP_001258502.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 102,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 309,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2592,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "WDR93",
          "gene_hgnc_id": 26924,
          "hgvs_c": "c.-41+203C>A",
          "hgvs_p": null,
          "transcript": "XM_011521794.3",
          "protein_id": "XP_011520096.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 725,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2178,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2350,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR93",
          "gene_hgnc_id": 26924,
          "hgvs_c": "c.-282C>A",
          "hgvs_p": null,
          "transcript": "NM_020212.2",
          "protein_id": "NP_064597.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 686,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2061,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2395,
          "mane_select": "ENST00000268130.12",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR93",
          "gene_hgnc_id": 26924,
          "hgvs_c": "c.-282C>A",
          "hgvs_p": null,
          "transcript": "ENST00000268130.12",
          "protein_id": "ENSP00000268130.7",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 686,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2061,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2395,
          "mane_select": "NM_020212.2",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR93",
          "gene_hgnc_id": 26924,
          "hgvs_c": "c.-282C>A",
          "hgvs_p": null,
          "transcript": "ENST00000558000.1",
          "protein_id": "ENSP00000453022.1",
          "transcript_support_level": 1,
          "aa_start": null,
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          "cds_start": -4,
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          "cdna_start": null,
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          "cdna_length": 1886,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
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        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR93",
          "gene_hgnc_id": 26924,
          "hgvs_c": "c.-282C>A",
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          "transcript": "NM_001284395.2",
          "protein_id": "NP_001271324.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": 658,
          "cds_start": -4,
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          "cdna_start": null,
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          "cdna_length": 2311,
          "mane_select": null,
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        },
        {
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          ],
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          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR93",
          "gene_hgnc_id": 26924,
          "hgvs_c": "c.-282C>A",
          "hgvs_p": null,
          "transcript": "ENST00000560294.5",
          "protein_id": "ENSP00000453971.1",
          "transcript_support_level": 2,
          "aa_start": null,
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          "aa_length": 658,
          "cds_start": -4,
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          "cdna_start": null,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
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          ],
          "exon_rank": null,
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          "exon_count": 3,
          "intron_rank": null,
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          "gene_symbol": "WDR93",
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          "hgvs_c": "c.-282C>A",
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        {
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          ],
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          "exon_count": 16,
          "intron_rank": null,
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          "gene_symbol": "WDR93",
          "gene_hgnc_id": 26924,
          "hgvs_c": "c.-282C>A",
          "hgvs_p": null,
          "transcript": "XM_006720614.2",
          "protein_id": "XP_006720677.1",
          "transcript_support_level": null,
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          "aa_length": 725,
          "cds_start": -4,
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
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          "consequences": [
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          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR93",
          "gene_hgnc_id": 26924,
          "hgvs_c": "c.-309C>A",
          "hgvs_p": null,
          "transcript": "XM_011521795.2",
          "protein_id": "XP_011520097.1",
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          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
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          "exon_count": 15,
          "intron_rank": null,
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          "gene_symbol": "WDR93",
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          "hgvs_c": "c.-282C>A",
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          "transcript": "XM_006720615.2",
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        {
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          ],
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          "exon_count": 16,
          "intron_rank": null,
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          "gene_symbol": "WDR93",
          "gene_hgnc_id": 26924,
          "hgvs_c": "c.-282C>A",
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          "transcript": "XM_011521796.3",
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        },
        {
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          "canonical": false,
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          "consequences": [
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          ],
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          "intron_rank": null,
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          "gene_symbol": "WDR93",
          "gene_hgnc_id": 26924,
          "hgvs_c": "c.-282C>A",
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          "transcript": "XM_006720618.2",
          "protein_id": "XP_006720681.1",
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          "aa_length": 468,
          "cds_start": -4,
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          "cdna_start": null,
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          "cdna_length": 1585,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR93",
          "gene_hgnc_id": 26924,
          "hgvs_c": "c.-282C>A",
          "hgvs_p": null,
          "transcript": "XM_047432869.1",
          "protein_id": "XP_047288825.1",
          "transcript_support_level": null,
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        {
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      ],
      "gene_symbol": "PEX11A",
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      "dbsnp": "rs373673442",
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      "hom_count_reference_population": 0,
      "allele_count_reference_population": 4,
      "gnomad_exomes_af": 0.00000285918,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 4,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.3698049783706665,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.221,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.183,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.31,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.919,
      "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": 1,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,BP4",
      "acmg_by_gene": [
        {
          "score": 1,
          "benign_score": 1,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000300056.8",
          "gene_symbol": "PEX11A",
          "hgnc_id": 8852,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.17G>T",
          "hgvs_p": "p.Arg6Leu"
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        {
          "score": 1,
          "benign_score": 1,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "XM_011521794.3",
          "gene_symbol": "WDR93",
          "hgnc_id": 26924,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.-41+203C>A",
          "hgvs_p": null
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      ],
      "clinvar_disease": "",
      "clinvar_classification": "",
      "clinvar_review_status": "",
      "clinvar_submissions_summary": "",
      "phenotype_combined": null,
      "pathogenicity_classification_combined": null,
      "custom_annotations": null
    }
  ],
  "message": null
}