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: 7-94412625-A-C (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=94412625&ref=A&alt=C&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "7",
      "pos": 94412625,
      "ref": "A",
      "alt": "C",
      "effect": "synonymous_variant",
      "transcript": "ENST00000297268.11",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 52,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL1A2",
          "gene_hgnc_id": 2198,
          "hgvs_c": "c.1446A>C",
          "hgvs_p": "p.Pro482Pro",
          "transcript": "NM_000089.4",
          "protein_id": "NP_000080.2",
          "transcript_support_level": null,
          "aa_start": 482,
          "aa_end": null,
          "aa_length": 1366,
          "cds_start": 1446,
          "cds_end": null,
          "cds_length": 4101,
          "cdna_start": 1583,
          "cdna_end": null,
          "cdna_length": 5072,
          "mane_select": "ENST00000297268.11",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 52,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL1A2",
          "gene_hgnc_id": 2198,
          "hgvs_c": "c.1446A>C",
          "hgvs_p": "p.Pro482Pro",
          "transcript": "ENST00000297268.11",
          "protein_id": "ENSP00000297268.6",
          "transcript_support_level": 1,
          "aa_start": 482,
          "aa_end": null,
          "aa_length": 1366,
          "cds_start": 1446,
          "cds_end": null,
          "cds_length": 4101,
          "cdna_start": 1583,
          "cdna_end": null,
          "cdna_length": 5072,
          "mane_select": "NM_000089.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "COL1A2",
      "gene_hgnc_id": 2198,
      "dbsnp": "rs412777",
      "frequency_reference_population": 0.35473987,
      "hom_count_reference_population": 102569,
      "allele_count_reference_population": 572365,
      "gnomad_exomes_af": 0.354784,
      "gnomad_genomes_af": 0.354314,
      "gnomad_exomes_ac": 518539,
      "gnomad_genomes_ac": 53826,
      "gnomad_exomes_homalt": 92959,
      "gnomad_genomes_homalt": 9610,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.6700000166893005,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.67,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.132,
      "phylop100way_prediction": "Benign",
      "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": -21,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
      "acmg_by_gene": [
        {
          "score": -21,
          "benign_score": 21,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BP7",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000297268.11",
          "gene_symbol": "COL1A2",
          "hgnc_id": 2198,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.1446A>C",
          "hgvs_p": "p.Pro482Pro"
        }
      ],
      "clinvar_disease": " 1, 2, arthrochalasia type, classic type, dominant form, perinatal lethal,Cardiovascular phenotype,Ehlers-Danlos syndrome,Osteogenesis imperfecta,Osteogenesis imperfecta type I,Osteogenesis imperfecta type III,Osteogenesis imperfecta with normal sclerae,not provided,not specified",
      "clinvar_classification": "Benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "B:12",
      "phenotype_combined": "Ehlers-Danlos syndrome, arthrochalasia type, 2|not specified|Osteogenesis imperfecta|Osteogenesis imperfecta type III|Osteogenesis imperfecta with normal sclerae, dominant form|Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1|Osteogenesis imperfecta, perinatal lethal|not provided|Cardiovascular phenotype",
      "pathogenicity_classification_combined": "Benign",
      "custom_annotations": null
    }
  ],
  "message": null
}