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: 6-31575254-G-A (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=31575254&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "message": null,
  "variants": [
    {
      "acmg_by_gene": [
        {
          "benign_score": 12,
          "criteria": [
            "BP4_Strong",
            "BA1"
          ],
          "effects": null,
          "gene_symbol": null,
          "hgnc_id": null,
          "hgvs_c": null,
          "hgvs_p": null,
          "inheritance_mode": "",
          "pathogenic_score": 0,
          "score": -12,
          "transcript": "",
          "verdict": "Benign"
        }
      ],
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BA1",
      "acmg_score": -12,
      "allele_count_reference_population": 62355,
      "alphamissense_prediction": null,
      "alphamissense_score": null,
      "alt": "A",
      "apogee2_prediction": null,
      "apogee2_score": null,
      "bayesdelnoaf_prediction": "Benign",
      "bayesdelnoaf_score": -0.82,
      "chr": "6",
      "clinvar_classification": "drug response",
      "clinvar_disease": " SUSCEPTIBILITY TO, TNFR, and/or TNFR4, cerebral, susceptibility to,Endometriosis,HUMAN IMMUNODEFICIENCY VIRUS DEMENTIA,Inherited susceptibility to asthma,Malaria,Psoriatic arthritis,Susceptibility to severe coronavirus disease (COVID-19),Susceptibility to severe coronavirus disease (COVID-19) due to high plasma levels of TNF,Systemic lupus erythematosus,etanercept response - Efficacy",
      "clinvar_review_status": "reviewed by expert panel",
      "clinvar_submissions_summary": "O:1",
      "computational_prediction_selected": "Benign",
      "computational_score_selected": -0.8199999928474426,
      "computational_source_selected": "BayesDel_noAF",
      "consequences": [],
      "custom_annotations": null,
      "dbscsnv_ada_prediction": null,
      "dbscsnv_ada_score": null,
      "dbsnp": "rs1800629",
      "effect": "",
      "frequency_reference_population": 0.13144359,
      "gene_hgnc_id": null,
      "gene_symbol": null,
      "gnomad_exomes_ac": 41363,
      "gnomad_exomes_af": 0.128353,
      "gnomad_exomes_homalt": 3225,
      "gnomad_genomes_ac": 20992,
      "gnomad_genomes_af": 0.137991,
      "gnomad_genomes_homalt": 1582,
      "gnomad_mito_heteroplasmic": null,
      "gnomad_mito_homoplasmic": null,
      "hom_count_reference_population": 4807,
      "mitotip_prediction": null,
      "mitotip_score": null,
      "pathogenicity_classification_combined": "drug response",
      "phenotype_combined": "etanercept response - Efficacy||Susceptibility to severe coronavirus disease (COVID-19) due to high plasma levels of TNF, TNFR, and/or TNFR4|Systemic lupus erythematosus, susceptibility to|Inherited susceptibility to asthma|Malaria, cerebral, susceptibility to||Susceptibility to severe coronavirus disease (COVID-19)|Endometriosis|HUMAN IMMUNODEFICIENCY VIRUS DEMENTIA, SUSCEPTIBILITY TO|Psoriatic arthritis, susceptibility to",
      "phylop100way_prediction": "Benign",
      "phylop100way_score": 0.018,
      "pos": 31575254,
      "ref": "G",
      "revel_prediction": null,
      "revel_score": null,
      "splice_prediction_selected": null,
      "splice_score_selected": null,
      "splice_source_selected": null,
      "spliceai_max_prediction": null,
      "spliceai_max_score": null,
      "transcript": null
    }
  ]
}