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: 17-63957197-C-T (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=63957197&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "17",
      "pos": 63957197,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000435607.3",
      "consequences": [
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SCN4A",
          "gene_hgnc_id": 10591,
          "hgvs_c": "c.2341G>A",
          "hgvs_p": "p.Val781Ile",
          "transcript": "NM_000334.4",
          "protein_id": "NP_000325.4",
          "transcript_support_level": null,
          "aa_start": 781,
          "aa_end": null,
          "aa_length": 1836,
          "cds_start": 2341,
          "cds_end": null,
          "cds_length": 5511,
          "cdna_start": 2418,
          "cdna_end": null,
          "cdna_length": 7805,
          "mane_select": "ENST00000435607.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SCN4A",
          "gene_hgnc_id": 10591,
          "hgvs_c": "c.2341G>A",
          "hgvs_p": "p.Val781Ile",
          "transcript": "ENST00000435607.3",
          "protein_id": "ENSP00000396320.1",
          "transcript_support_level": 1,
          "aa_start": 781,
          "aa_end": null,
          "aa_length": 1836,
          "cds_start": 2341,
          "cds_end": null,
          "cds_length": 5511,
          "cdna_start": 2418,
          "cdna_end": null,
          "cdna_length": 7805,
          "mane_select": "NM_000334.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "SCN4A",
      "gene_hgnc_id": 10591,
      "dbsnp": "rs62070884",
      "frequency_reference_population": 0.007712229,
      "hom_count_reference_population": 77,
      "allele_count_reference_population": 12269,
      "gnomad_exomes_af": 0.0076056,
      "gnomad_genomes_af": 0.0087194,
      "gnomad_exomes_ac": 10941,
      "gnomad_genomes_ac": 1328,
      "gnomad_exomes_homalt": 70,
      "gnomad_genomes_homalt": 7,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.015130966901779175,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.73,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.164,
      "alphamissense_prediction": "Benign",
      "bayesdelnoaf_score": 0.19,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 7.905,
      "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": -19,
      "acmg_classification": "Benign",
      "acmg_criteria": "PP2,BP4_Strong,BP6_Very_Strong,BS1,BS2",
      "acmg_by_gene": [
        {
          "score": -19,
          "benign_score": 20,
          "pathogenic_score": 1,
          "criteria": [
            "PP2",
            "BP4_Strong",
            "BP6_Very_Strong",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000435607.3",
          "gene_symbol": "SCN4A",
          "hgnc_id": 10591,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "c.2341G>A",
          "hgvs_p": "p.Val781Ile"
        }
      ],
      "clinvar_disease": " type 2,6 conditions,Congenital myasthenic syndrome 16,Familial hyperkalemic periodic paralysis,Hypokalemic periodic paralysis,Joubert syndrome 17,Paramyotonia congenita of Von Eulenburg,Potassium-aggravated myotonia,not provided,not specified",
      "clinvar_classification": "Benign/Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:10 B:6 O:1",
      "phenotype_combined": "Familial hyperkalemic periodic paralysis|Congenital myasthenic syndrome 16|Paramyotonia congenita of Von Eulenburg|not specified|Hypokalemic periodic paralysis, type 2|not provided|Potassium-aggravated myotonia|Joubert syndrome 17|6 conditions",
      "pathogenicity_classification_combined": "Benign/Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}