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: 7-94409367-G-A (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=94409367&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "7",
      "pos": 94409367,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "ENST00000297268.11",
      "consequences": [
        {
          "aa_ref": "G",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 52,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL1A2",
          "gene_hgnc_id": 2198,
          "hgvs_c": "c.838G>A",
          "hgvs_p": "p.Gly280Ser",
          "transcript": "NM_000089.4",
          "protein_id": "NP_000080.2",
          "transcript_support_level": null,
          "aa_start": 280,
          "aa_end": null,
          "aa_length": 1366,
          "cds_start": 838,
          "cds_end": null,
          "cds_length": 4101,
          "cdna_start": 975,
          "cdna_end": null,
          "cdna_length": 5072,
          "mane_select": "ENST00000297268.11",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "G",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 52,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL1A2",
          "gene_hgnc_id": 2198,
          "hgvs_c": "c.838G>A",
          "hgvs_p": "p.Gly280Ser",
          "transcript": "ENST00000297268.11",
          "protein_id": "ENSP00000297268.6",
          "transcript_support_level": 1,
          "aa_start": 280,
          "aa_end": null,
          "aa_length": 1366,
          "cds_start": 838,
          "cds_end": null,
          "cds_length": 4101,
          "cdna_start": 975,
          "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": "rs72656387",
      "frequency_reference_population": 0.0000037174077,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 6,
      "gnomad_exomes_af": 0.00000342023,
      "gnomad_genomes_af": 0.00000657289,
      "gnomad_exomes_ac": 5,
      "gnomad_genomes_ac": 1,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.9941796064376831,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.984,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.8501,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.59,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 9.84,
      "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": 17,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PM1,PM5,PP2,PP3_Strong,PP5_Very_Strong",
      "acmg_by_gene": [
        {
          "score": 17,
          "benign_score": 0,
          "pathogenic_score": 17,
          "criteria": [
            "PM1",
            "PM5",
            "PP2",
            "PP3_Strong",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000297268.11",
          "gene_symbol": "COL1A2",
          "hgnc_id": 2198,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.838G>A",
          "hgvs_p": "p.Gly280Ser"
        }
      ],
      "clinvar_disease": " 1, 2, arthrochalasia type, classic type, perinatal lethal,7 conditions,COL1A2-related disorder,Cardiovascular phenotype,Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 2,Ehlers-Danlos syndrome,Increased susceptibility to fractures,Osteogenesis imperfecta,Osteogenesis imperfecta type I,not provided",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "P:13",
      "phenotype_combined": "Osteogenesis imperfecta|not provided|Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 2|Ehlers-Danlos syndrome, arthrochalasia type, 2|Osteogenesis imperfecta, perinatal lethal|Ehlers-Danlos syndrome, classic type, 1;Osteogenesis imperfecta type I|Increased susceptibility to fractures|Cardiovascular phenotype|COL1A2-related disorder|7 conditions",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}