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: 13-27920235-C-A (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=27920235&ref=C&alt=A&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "13",
      "pos": 27920235,
      "ref": "C",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "ENST00000381033.5",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDX1",
          "gene_hgnc_id": 6107,
          "hgvs_c": "c.97C>A",
          "hgvs_p": "p.Pro33Thr",
          "transcript": "NM_000209.4",
          "protein_id": "NP_000200.1",
          "transcript_support_level": null,
          "aa_start": 33,
          "aa_end": null,
          "aa_length": 283,
          "cds_start": 97,
          "cds_end": null,
          "cds_length": 852,
          "cdna_start": 236,
          "cdna_end": null,
          "cdna_length": 2603,
          "mane_select": "ENST00000381033.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDX1",
          "gene_hgnc_id": 6107,
          "hgvs_c": "c.97C>A",
          "hgvs_p": "p.Pro33Thr",
          "transcript": "ENST00000381033.5",
          "protein_id": "ENSP00000370421.4",
          "transcript_support_level": 1,
          "aa_start": 33,
          "aa_end": null,
          "aa_length": 283,
          "cds_start": 97,
          "cds_end": null,
          "cds_length": 852,
          "cdna_start": 236,
          "cdna_end": null,
          "cdna_length": 2603,
          "mane_select": "NM_000209.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "PDX1",
      "gene_hgnc_id": 6107,
      "dbsnp": "rs192902098",
      "frequency_reference_population": 0.0019905267,
      "hom_count_reference_population": 17,
      "allele_count_reference_population": 3082,
      "gnomad_exomes_af": 0.00201139,
      "gnomad_genomes_af": 0.00179925,
      "gnomad_exomes_ac": 2808,
      "gnomad_genomes_ac": 274,
      "gnomad_exomes_homalt": 15,
      "gnomad_genomes_homalt": 2,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.034783631563186646,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.928,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.7249,
      "alphamissense_prediction": "Pathogenic",
      "bayesdelnoaf_score": 0.43,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 5.585,
      "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": -12,
      "acmg_classification": "Benign",
      "acmg_criteria": "PP2,BP4_Strong,BP6,BS1,BS2",
      "acmg_by_gene": [
        {
          "score": -12,
          "benign_score": 13,
          "pathogenic_score": 1,
          "criteria": [
            "PP2",
            "BP4_Strong",
            "BP6",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000381033.5",
          "gene_symbol": "PDX1",
          "hgnc_id": 6107,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "c.97C>A",
          "hgvs_p": "p.Pro33Thr"
        }
      ],
      "clinvar_disease": "Maturity onset diabetes mellitus in young,Maturity-onset diabetes of the young type 4,Monogenic diabetes,Type 2 diabetes mellitus,not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:4 LB:2 B:3",
      "phenotype_combined": "not specified|not provided|Maturity-onset diabetes of the young type 4|Type 2 diabetes mellitus|Monogenic diabetes|Maturity onset diabetes mellitus in young",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}