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: 11-1219991-G-T (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=1219991&ref=G&alt=T&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "11",
      "pos": 1219991,
      "ref": "G",
      "alt": "T",
      "effect": "splice_region_variant,non_coding_transcript_exon_variant",
      "transcript": "ENST00000654177.1",
      "consequences": [
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "splice_region_variant",
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000286275",
          "gene_hgnc_id": null,
          "hgvs_c": "n.661G>T",
          "hgvs_p": null,
          "transcript": "ENST00000654177.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 912,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "ENSG00000286275",
      "gene_hgnc_id": null,
      "dbsnp": "rs35705950",
      "frequency_reference_population": 0.0793194,
      "hom_count_reference_population": 596,
      "allele_count_reference_population": 12074,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": 0.0793194,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": 12074,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": 596,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.6800000071525574,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": null,
      "splice_prediction_selected": null,
      "splice_source_selected": null,
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.68,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.183,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": null,
      "spliceai_max_prediction": null,
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": -20,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
      "acmg_by_gene": [
        {
          "score": -20,
          "benign_score": 20,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000654177.1",
          "gene_symbol": "ENSG00000286275",
          "hgnc_id": null,
          "effects": [
            "splice_region_variant",
            "non_coding_transcript_exon_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.661G>T",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " idiopathic, susceptibility to,Antisynthetase syndrome,Interstitial lung disease 2,Pulmonary fibrosis,Susceptibility to coronavirus disease (COVID-19) severity and mortality due to low plasma levels of MUC5B,not provided",
      "clinvar_classification": " risk factor,Benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "B:1 O:1",
      "phenotype_combined": "Pulmonary fibrosis, idiopathic, susceptibility to|Interstitial lung disease 2|not provided|Susceptibility to coronavirus disease (COVID-19) severity and mortality due to low plasma levels of MUC5B|Antisynthetase syndrome",
      "pathogenicity_classification_combined": "Benign; risk factor",
      "custom_annotations": null
    }
  ],
  "message": null
}