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: 10-71793370-G-A (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=71793370&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "10",
      "pos": 71793370,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "ENST00000224721.12",
      "consequences": [
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 48,
          "exon_rank_end": null,
          "exon_count": 70,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDH23",
          "gene_hgnc_id": 13733,
          "hgvs_c": "c.6442G>A",
          "hgvs_p": "p.Asp2148Asn",
          "transcript": "NM_022124.6",
          "protein_id": "NP_071407.4",
          "transcript_support_level": null,
          "aa_start": 2148,
          "aa_end": null,
          "aa_length": 3354,
          "cds_start": 6442,
          "cds_end": null,
          "cds_length": 10065,
          "cdna_start": 6846,
          "cdna_end": null,
          "cdna_length": 11138,
          "mane_select": "ENST00000224721.12",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 48,
          "exon_rank_end": null,
          "exon_count": 70,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDH23",
          "gene_hgnc_id": 13733,
          "hgvs_c": "c.6442G>A",
          "hgvs_p": "p.Asp2148Asn",
          "transcript": "ENST00000224721.12",
          "protein_id": "ENSP00000224721.9",
          "transcript_support_level": 5,
          "aa_start": 2148,
          "aa_end": null,
          "aa_length": 3354,
          "cds_start": 6442,
          "cds_end": null,
          "cds_length": 10065,
          "cdna_start": 6846,
          "cdna_end": null,
          "cdna_length": 11138,
          "mane_select": "NM_022124.6",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "CDH23",
      "gene_hgnc_id": 13733,
      "dbsnp": "rs111033271",
      "frequency_reference_population": 0.00008984971,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 145,
      "gnomad_exomes_af": 0.0000896228,
      "gnomad_genomes_af": 0.0000920302,
      "gnomad_exomes_ac": 131,
      "gnomad_genomes_ac": 14,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.8468902707099915,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.731,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.5702,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.15,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 9.906,
      "phylop100way_prediction": "Pathogenic",
      "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": "Pathogenic",
      "acmg_criteria": "PM2,PP3_Moderate,PP5_Very_Strong",
      "acmg_by_gene": [
        {
          "score": 12,
          "benign_score": 0,
          "pathogenic_score": 12,
          "criteria": [
            "PM2",
            "PP3_Moderate",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000224721.12",
          "gene_symbol": "CDH23",
          "hgnc_id": 13733,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.6442G>A",
          "hgvs_p": "p.Asp2148Asn"
        }
      ],
      "clinvar_disease": " multiple types,Autosomal recessive nonsyndromic hearing loss 12,CDH23-related disorder,Pituitary adenoma 5,Rare genetic deafness,Retinal dystrophy,Usher syndrome,Usher syndrome type 1,Usher syndrome type 1D,Usher syndrome type 2A,not provided",
      "clinvar_classification": "Pathogenic/Likely pathogenic",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "P:9 LP:3",
      "phenotype_combined": "Autosomal recessive nonsyndromic hearing loss 12|Rare genetic deafness|Usher syndrome type 2A;Autosomal recessive nonsyndromic hearing loss 12|not provided|Usher syndrome type 1|Usher syndrome|Pituitary adenoma 5, multiple types|CDH23-related disorder|Retinal dystrophy|Usher syndrome type 1D|Usher syndrome type 1D;Pituitary adenoma 5, multiple types;Autosomal recessive nonsyndromic hearing loss 12",
      "pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}