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-25013530-G-GGCCGCGGCGGCCGCGGCCGCGGCT (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=25013530&ref=G&alt=GGCCGCGGCGGCCGCGGCCGCGGCT&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "X",
      "pos": 25013530,
      "ref": "G",
      "alt": "GGCCGCGGCGGCCGCGGCCGCGGCT",
      "effect": "disruptive_inframe_insertion",
      "transcript": "ENST00000379044.5",
      "consequences": [
        {
          "aa_ref": "A",
          "aa_alt": "AAAAAAAAA",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "disruptive_inframe_insertion"
          ],
          "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.441_464dupAGCCGCGGCCGCGGCCGCCGCGGC",
          "hgvs_p": "p.Ala148_Ala155dup",
          "transcript": "NM_139058.3",
          "protein_id": "NP_620689.1",
          "transcript_support_level": null,
          "aa_start": 155,
          "aa_end": null,
          "aa_length": 562,
          "cds_start": 464,
          "cds_end": null,
          "cds_length": 1689,
          "cdna_start": 692,
          "cdna_end": null,
          "cdna_length": 2893,
          "mane_select": "ENST00000379044.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "AAAAAAAAA",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "disruptive_inframe_insertion"
          ],
          "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.441_464dupAGCCGCGGCCGCGGCCGCCGCGGC",
          "hgvs_p": "p.Ala148_Ala155dup",
          "transcript": "ENST00000379044.5",
          "protein_id": "ENSP00000368332.4",
          "transcript_support_level": 1,
          "aa_start": 155,
          "aa_end": null,
          "aa_length": 562,
          "cds_start": 464,
          "cds_end": null,
          "cds_length": 1689,
          "cdna_start": 692,
          "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": "rs398124510",
      "frequency_reference_population": 0.0000024574342,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 2,
      "gnomad_exomes_af": 0.00000141006,
      "gnomad_genomes_af": 0.00000955402,
      "gnomad_exomes_ac": 1,
      "gnomad_genomes_ac": 1,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": null,
      "computational_prediction_selected": null,
      "computational_source_selected": null,
      "splice_score_selected": null,
      "splice_prediction_selected": null,
      "splice_source_selected": null,
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": null,
      "bayesdelnoaf_prediction": null,
      "phylop100way_score": 0.378,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": null,
      "spliceai_max_prediction": null,
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": 10,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PM4,PP5_Very_Strong",
      "acmg_by_gene": [
        {
          "score": 10,
          "benign_score": 0,
          "pathogenic_score": 10,
          "criteria": [
            "PM4",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000379044.5",
          "gene_symbol": "ARX",
          "hgnc_id": 18060,
          "effects": [
            "disruptive_inframe_insertion"
          ],
          "inheritance_mode": "AD,XL",
          "hgvs_c": "c.441_464dupAGCCGCGGCCGCGGCCGCCGCGGC",
          "hgvs_p": "p.Ala148_Ala155dup"
        }
      ],
      "clinvar_disease": " 1, ARX-related, X-linked, with or without seizures,Corpus callosum agenesis-abnormal genitalia syndrome,Developmental and epileptic encephalopathy,Intellectual disability,Partington syndrome,X-linked lissencephaly with abnormal genitalia,not provided",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "P:6",
      "phenotype_combined": "not provided|X-linked lissencephaly with abnormal genitalia|Intellectual disability, X-linked, with or without seizures, ARX-related;Developmental and epileptic encephalopathy, 1|Partington syndrome;Intellectual disability, X-linked, with or without seizures, ARX-related;Developmental and epileptic encephalopathy, 1;Corpus callosum agenesis-abnormal genitalia syndrome;X-linked lissencephaly with abnormal genitalia",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}