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: 13-27924562-T-TGCC (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=27924562&ref=T&alt=TGCC&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "13",
      "pos": 27924562,
      "ref": "T",
      "alt": "TGCC",
      "effect": "disruptive_inframe_insertion",
      "transcript": "ENST00000381033.5",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "PP",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "disruptive_inframe_insertion"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDX1",
          "gene_hgnc_id": 6107,
          "hgvs_c": "c.726_728dupGCC",
          "hgvs_p": "p.Pro243dup",
          "transcript": "NM_000209.4",
          "protein_id": "NP_000200.1",
          "transcript_support_level": null,
          "aa_start": 243,
          "aa_end": null,
          "aa_length": 283,
          "cds_start": 729,
          "cds_end": null,
          "cds_length": 852,
          "cdna_start": 868,
          "cdna_end": null,
          "cdna_length": 2603,
          "mane_select": "ENST00000381033.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "PP",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "disruptive_inframe_insertion"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDX1",
          "gene_hgnc_id": 6107,
          "hgvs_c": "c.726_728dupGCC",
          "hgvs_p": "p.Pro243dup",
          "transcript": "ENST00000381033.5",
          "protein_id": "ENSP00000370421.4",
          "transcript_support_level": 1,
          "aa_start": 243,
          "aa_end": null,
          "aa_length": 283,
          "cds_start": 729,
          "cds_end": null,
          "cds_length": 852,
          "cdna_start": 868,
          "cdna_end": null,
          "cdna_length": 2603,
          "mane_select": "NM_000209.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "PDX1",
      "gene_hgnc_id": 6107,
      "dbsnp": "rs193922357",
      "frequency_reference_population": 0.0044962,
      "hom_count_reference_population": 253,
      "allele_count_reference_population": 6897,
      "gnomad_exomes_af": 0.00223473,
      "gnomad_genomes_af": 0.0250365,
      "gnomad_exomes_ac": 3088,
      "gnomad_genomes_ac": 3809,
      "gnomad_exomes_homalt": 103,
      "gnomad_genomes_homalt": 150,
      "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": 0.781,
      "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": -8,
      "acmg_classification": "Benign",
      "acmg_criteria": "PM4_Supporting,BP6,BA1",
      "acmg_by_gene": [
        {
          "score": -8,
          "benign_score": 9,
          "pathogenic_score": 1,
          "criteria": [
            "PM4_Supporting",
            "BP6",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000381033.5",
          "gene_symbol": "PDX1",
          "hgnc_id": 6107,
          "effects": [
            "disruptive_inframe_insertion"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "c.726_728dupGCC",
          "hgvs_p": "p.Pro243dup"
        }
      ],
      "clinvar_disease": " susceptibility to,Diabetes mellitus type 2,Maturity onset diabetes mellitus in young,Maturity-onset diabetes of the young type 4,Monogenic diabetes,Neonatal diabetes mellitus,not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:1 B:9",
      "phenotype_combined": "Maturity-onset diabetes of the young type 4|Neonatal diabetes mellitus|not specified|Monogenic diabetes|Diabetes mellitus type 2, susceptibility to|not provided|Maturity onset diabetes mellitus in young",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}