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: 7-94404580-C-T (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=94404580&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "7",
      "pos": 94404580,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000297268.11",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 52,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL1A2",
          "gene_hgnc_id": 2198,
          "hgvs_c": "c.304C>T",
          "hgvs_p": "p.Pro102Ser",
          "transcript": "NM_000089.4",
          "protein_id": "NP_000080.2",
          "transcript_support_level": null,
          "aa_start": 102,
          "aa_end": null,
          "aa_length": 1366,
          "cds_start": 304,
          "cds_end": null,
          "cds_length": 4101,
          "cdna_start": 441,
          "cdna_end": null,
          "cdna_length": 5072,
          "mane_select": "ENST00000297268.11",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 52,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL1A2",
          "gene_hgnc_id": 2198,
          "hgvs_c": "c.304C>T",
          "hgvs_p": "p.Pro102Ser",
          "transcript": "ENST00000297268.11",
          "protein_id": "ENSP00000297268.6",
          "transcript_support_level": 1,
          "aa_start": 102,
          "aa_end": null,
          "aa_length": 1366,
          "cds_start": 304,
          "cds_end": null,
          "cds_length": 4101,
          "cdna_start": 441,
          "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": "rs189557655",
      "frequency_reference_population": 0.00067172234,
      "hom_count_reference_population": 1,
      "allele_count_reference_population": 1084,
      "gnomad_exomes_af": 0.000684251,
      "gnomad_genomes_af": 0.000551507,
      "gnomad_exomes_ac": 1000,
      "gnomad_genomes_ac": 84,
      "gnomad_exomes_homalt": 1,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.10725909471511841,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.405,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.068,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.1,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 3.734,
      "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": 0,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM1,PP2,BP4_Moderate,BP6",
      "acmg_by_gene": [
        {
          "score": 0,
          "benign_score": 3,
          "pathogenic_score": 3,
          "criteria": [
            "PM1",
            "PP2",
            "BP4_Moderate",
            "BP6"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000297268.11",
          "gene_symbol": "COL1A2",
          "hgnc_id": 2198,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.304C>T",
          "hgvs_p": "p.Pro102Ser"
        }
      ],
      "clinvar_disease": " 1, 2, arthrochalasia type, classic type,Cardiovascular phenotype,Connective tissue disorder,Ehlers-Danlos syndrome,Osteogenesis imperfecta,Osteogenesis imperfecta type I,not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:2 LB:8 B:3",
      "phenotype_combined": "Connective tissue disorder|not provided|Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1|not specified|Osteogenesis imperfecta|Ehlers-Danlos syndrome, arthrochalasia type, 2|Cardiovascular phenotype|Ehlers-Danlos syndrome",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}