← Back to variant description

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: 2-120019167-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=120019167&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "2",
      "pos": 120019167,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_020909.4",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "NM_020909.4",
          "protein_id": "NP_065960.2",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 733,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 2202,
          "cdna_start": 225,
          "cdna_end": null,
          "cdna_length": 6556,
          "mane_select": "ENST00000263713.10",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "ENST00000263713.10",
          "protein_id": "ENSP00000263713.5",
          "transcript_support_level": 1,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 733,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 2202,
          "cdna_start": 225,
          "cdna_end": null,
          "cdna_length": 6556,
          "mane_select": "NM_020909.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "ENST00000443124.5",
          "protein_id": "ENSP00000393722.1",
          "transcript_support_level": 1,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 505,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1518,
          "cdna_start": 562,
          "cdna_end": null,
          "cdna_length": 2872,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "NM_001330310.2",
          "protein_id": "NP_001317239.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 732,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 2199,
          "cdna_start": 225,
          "cdna_end": null,
          "cdna_length": 6553,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "ENST00000452780.1",
          "protein_id": "ENSP00000390439.1",
          "transcript_support_level": 5,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 732,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 2199,
          "cdna_start": 83,
          "cdna_end": null,
          "cdna_length": 6410,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "NM_001184937.2",
          "protein_id": "NP_001171866.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 687,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 2064,
          "cdna_start": 225,
          "cdna_end": null,
          "cdna_length": 6425,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "ENST00000443902.6",
          "protein_id": "ENSP00000393856.2",
          "transcript_support_level": 2,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 687,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 2064,
          "cdna_start": 225,
          "cdna_end": null,
          "cdna_length": 3167,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "NM_001184938.4",
          "protein_id": "NP_001171867.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 505,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1518,
          "cdna_start": 696,
          "cdna_end": null,
          "cdna_length": 6365,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "NM_001184939.3",
          "protein_id": "NP_001171868.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 505,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1518,
          "cdna_start": 225,
          "cdna_end": null,
          "cdna_length": 5894,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "ENST00000331393.8",
          "protein_id": "ENSP00000329687.4",
          "transcript_support_level": 2,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 505,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 1518,
          "cdna_start": 183,
          "cdna_end": null,
          "cdna_length": 1777,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "XM_006712651.2",
          "protein_id": "XP_006712714.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 740,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 2223,
          "cdna_start": 225,
          "cdna_end": null,
          "cdna_length": 6577,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "XM_017004567.1",
          "protein_id": "XP_016860056.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 740,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 2223,
          "cdna_start": 110,
          "cdna_end": null,
          "cdna_length": 6462,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "XM_047445208.1",
          "protein_id": "XP_047301164.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 740,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 2223,
          "cdna_start": 696,
          "cdna_end": null,
          "cdna_length": 7048,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His",
          "transcript": "XM_047445210.1",
          "protein_id": "XP_047301166.1",
          "transcript_support_level": null,
          "aa_start": 28,
          "aa_end": null,
          "aa_length": 733,
          "cds_start": 83,
          "cds_end": null,
          "cds_length": 2202,
          "cdna_start": 696,
          "cdna_end": null,
          "cdna_length": 7027,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "n.20G>A",
          "hgvs_p": null,
          "transcript": "ENST00000466241.1",
          "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": 566,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "n.225G>A",
          "hgvs_p": null,
          "transcript": "NR_135920.3",
          "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": 5997,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "n.225G>A",
          "hgvs_p": null,
          "transcript": "NR_138472.2",
          "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": 6025,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "5_prime_UTR_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.-138G>A",
          "hgvs_p": null,
          "transcript": "NM_001330307.2",
          "protein_id": "NP_001317236.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 433,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 1302,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5898,
          "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": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "EPB41L5",
          "gene_hgnc_id": 19819,
          "hgvs_c": "c.-138G>A",
          "hgvs_p": null,
          "transcript": "XM_006712653.2",
          "protein_id": "XP_006712716.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 668,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2007,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6343,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "EPB41L5",
      "gene_hgnc_id": 19819,
      "dbsnp": "rs758913196",
      "frequency_reference_population": 0.000009294509,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 15,
      "gnomad_exomes_af": 0.00000820868,
      "gnomad_genomes_af": 0.0000197384,
      "gnomad_exomes_ac": 12,
      "gnomad_genomes_ac": 3,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.42207860946655273,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.383,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.1931,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.16,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 7.507,
      "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": 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": "NM_020909.4",
          "gene_symbol": "EPB41L5",
          "hgnc_id": 19819,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.83G>A",
          "hgvs_p": "p.Arg28His"
        }
      ],
      "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
}