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: 6-117693132-C-G (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=117693132&ref=C&alt=G&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "6",
      "pos": 117693132,
      "ref": "C",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000368494.4",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NUS1",
          "gene_hgnc_id": 21042,
          "hgvs_c": "c.506C>G",
          "hgvs_p": "p.Pro169Arg",
          "transcript": "NM_138459.5",
          "protein_id": "NP_612468.1",
          "transcript_support_level": null,
          "aa_start": 169,
          "aa_end": null,
          "aa_length": 293,
          "cds_start": 506,
          "cds_end": null,
          "cds_length": 882,
          "cdna_start": 708,
          "cdna_end": null,
          "cdna_length": 4796,
          "mane_select": "ENST00000368494.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NUS1",
          "gene_hgnc_id": 21042,
          "hgvs_c": "c.506C>G",
          "hgvs_p": "p.Pro169Arg",
          "transcript": "ENST00000368494.4",
          "protein_id": "ENSP00000357480.3",
          "transcript_support_level": 1,
          "aa_start": 169,
          "aa_end": null,
          "aa_length": 293,
          "cds_start": 506,
          "cds_end": null,
          "cds_length": 882,
          "cdna_start": 708,
          "cdna_end": null,
          "cdna_length": 4796,
          "mane_select": "NM_138459.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "NUS1",
      "gene_hgnc_id": 21042,
      "dbsnp": "rs150646335",
      "frequency_reference_population": 0.0016001131,
      "hom_count_reference_population": 7,
      "allele_count_reference_population": 2580,
      "gnomad_exomes_af": 0.00165027,
      "gnomad_genomes_af": 0.00111827,
      "gnomad_exomes_ac": 2410,
      "gnomad_genomes_ac": 170,
      "gnomad_exomes_homalt": 7,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.008862853050231934,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.025,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.1463,
      "alphamissense_prediction": "Benign",
      "bayesdelnoaf_score": -0.54,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 1.829,
      "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": -9,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6,BS2",
      "acmg_by_gene": [
        {
          "score": -9,
          "benign_score": 9,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000368494.4",
          "gene_symbol": "NUS1",
          "hgnc_id": 21042,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.506C>G",
          "hgvs_p": "p.Pro169Arg"
        }
      ],
      "clinvar_disease": " autosomal dominant 55, type IAA, with seizures,Congenital disorder of glycosylation,Intellectual disability,NUS1-related disorder,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:1 LB:2",
      "phenotype_combined": "Congenital disorder of glycosylation, type IAA|Intellectual disability, autosomal dominant 55, with seizures|not provided|NUS1-related disorder",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}