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: 1-228158992-C-T (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=228158992&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "1",
      "pos": 228158992,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000366714.3",
      "consequences": [
        {
          "aa_ref": "H",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GJC2",
          "gene_hgnc_id": 17494,
          "hgvs_c": "c.1234C>T",
          "hgvs_p": "p.His412Tyr",
          "transcript": "NM_020435.4",
          "protein_id": "NP_065168.2",
          "transcript_support_level": null,
          "aa_start": 412,
          "aa_end": null,
          "aa_length": 439,
          "cds_start": 1234,
          "cds_end": null,
          "cds_length": 1320,
          "cdna_start": 1331,
          "cdna_end": null,
          "cdna_length": 2165,
          "mane_select": "ENST00000366714.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "H",
          "aa_alt": "Y",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GJC2",
          "gene_hgnc_id": 17494,
          "hgvs_c": "c.1234C>T",
          "hgvs_p": "p.His412Tyr",
          "transcript": "ENST00000366714.3",
          "protein_id": "ENSP00000355675.2",
          "transcript_support_level": 1,
          "aa_start": 412,
          "aa_end": null,
          "aa_length": 439,
          "cds_start": 1234,
          "cds_end": null,
          "cds_length": 1320,
          "cdna_start": 1331,
          "cdna_end": null,
          "cdna_length": 2165,
          "mane_select": "NM_020435.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "GJC2",
      "gene_hgnc_id": 17494,
      "dbsnp": "rs200334298",
      "frequency_reference_population": 0.0009559621,
      "hom_count_reference_population": 3,
      "allele_count_reference_population": 1533,
      "gnomad_exomes_af": 0.000959036,
      "gnomad_genomes_af": 0.000926644,
      "gnomad_exomes_ac": 1392,
      "gnomad_genomes_ac": 141,
      "gnomad_exomes_homalt": 3,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.089141845703125,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.5,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.0953,
      "alphamissense_prediction": "Benign",
      "bayesdelnoaf_score": 0.15,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 4.831,
      "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": -5,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "PP2,BP4_Moderate,BS2",
      "acmg_by_gene": [
        {
          "score": -5,
          "benign_score": 6,
          "pathogenic_score": 1,
          "criteria": [
            "PP2",
            "BP4_Moderate",
            "BS2"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000366714.3",
          "gene_symbol": "GJC2",
          "hgnc_id": 17494,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "c.1234C>T",
          "hgvs_p": "p.His412Tyr"
        }
      ],
      "clinvar_disease": "Hereditary spastic paraplegia,Hereditary spastic paraplegia 44,Hypomyelinating leukodystrophy 2,Inborn genetic diseases,Lymphatic malformation 3,Spastic paraplegia,not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:10 LB:1",
      "phenotype_combined": "not provided|Hypomyelinating leukodystrophy 2;Lymphatic malformation 3;Hereditary spastic paraplegia 44|Spastic paraplegia|Inborn genetic diseases|not specified|Hereditary spastic paraplegia|Hypomyelinating leukodystrophy 2",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}