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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: X-25013370-C-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=25013370&ref=C&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "X",
      "pos": 25013370,
      "ref": "C",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000379044.5",
      "consequences": [
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ARX",
          "gene_hgnc_id": 18060,
          "hgvs_c": "c.625G>C",
          "hgvs_p": "p.Gly209Arg",
          "transcript": "NM_139058.3",
          "protein_id": "NP_620689.1",
          "transcript_support_level": null,
          "aa_start": 209,
          "aa_end": null,
          "aa_length": 562,
          "cds_start": 625,
          "cds_end": null,
          "cds_length": 1689,
          "cdna_start": 853,
          "cdna_end": null,
          "cdna_length": 2893,
          "mane_select": "ENST00000379044.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ARX",
          "gene_hgnc_id": 18060,
          "hgvs_c": "c.625G>C",
          "hgvs_p": "p.Gly209Arg",
          "transcript": "ENST00000379044.5",
          "protein_id": "ENSP00000368332.4",
          "transcript_support_level": 1,
          "aa_start": 209,
          "aa_end": null,
          "aa_length": 562,
          "cds_start": 625,
          "cds_end": null,
          "cds_length": 1689,
          "cdna_start": 853,
          "cdna_end": null,
          "cdna_length": 2893,
          "mane_select": "NM_139058.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "ARX",
      "gene_hgnc_id": 18060,
      "dbsnp": "rs587783203",
      "frequency_reference_population": 0.0000808438,
      "hom_count_reference_population": 22,
      "allele_count_reference_population": 92,
      "gnomad_exomes_af": 0.0000855551,
      "gnomad_genomes_af": 0.0000365564,
      "gnomad_exomes_ac": 88,
      "gnomad_genomes_ac": 4,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.12503540515899658,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.27,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.1606,
      "alphamissense_prediction": "Benign",
      "bayesdelnoaf_score": -0.31,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.224,
      "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": -7,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Moderate,BP6,BS2",
      "acmg_by_gene": [
        {
          "score": -7,
          "benign_score": 7,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Moderate",
            "BP6",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000379044.5",
          "gene_symbol": "ARX",
          "hgnc_id": 18060,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,XL",
          "hgvs_c": "c.625G>C",
          "hgvs_p": "p.Gly209Arg"
        }
      ],
      "clinvar_disease": " 1, ARX-related, X-linked, early infanitle, with or without seizures,Developmental and epileptic encephalopathy,Intellectual disability,epileptic encephalopathy,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:2 LB:1",
      "phenotype_combined": "epileptic encephalopathy, early infanitle, 1|not provided|Developmental and epileptic encephalopathy, 1;Intellectual disability, X-linked, with or without seizures, ARX-related",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}