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: 14-23389478-G-A (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=23389478&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "14",
      "pos": 23389478,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "ENST00000405093.9",
      "consequences": [
        {
          "aa_ref": "A",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 28,
          "exon_rank_end": null,
          "exon_count": 39,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYH6",
          "gene_hgnc_id": 7576,
          "hgvs_c": "c.3893C>T",
          "hgvs_p": "p.Ala1298Val",
          "transcript": "NM_002471.4",
          "protein_id": "NP_002462.2",
          "transcript_support_level": null,
          "aa_start": 1298,
          "aa_end": null,
          "aa_length": 1939,
          "cds_start": 3893,
          "cds_end": null,
          "cds_length": 5820,
          "cdna_start": 3960,
          "cdna_end": null,
          "cdna_length": 5940,
          "mane_select": "ENST00000405093.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "V",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 28,
          "exon_rank_end": null,
          "exon_count": 39,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYH6",
          "gene_hgnc_id": 7576,
          "hgvs_c": "c.3893C>T",
          "hgvs_p": "p.Ala1298Val",
          "transcript": "ENST00000405093.9",
          "protein_id": "ENSP00000386041.3",
          "transcript_support_level": 5,
          "aa_start": 1298,
          "aa_end": null,
          "aa_length": 1939,
          "cds_start": 3893,
          "cds_end": null,
          "cds_length": 5820,
          "cdna_start": 3960,
          "cdna_end": null,
          "cdna_length": 5940,
          "mane_select": "NM_002471.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "MYH6",
      "gene_hgnc_id": 7576,
      "dbsnp": "rs368588052",
      "frequency_reference_population": 0.00014436201,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 233,
      "gnomad_exomes_af": 0.000147754,
      "gnomad_genomes_af": 0.000111761,
      "gnomad_exomes_ac": 216,
      "gnomad_genomes_ac": 17,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.14300104975700378,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.019999999552965164,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.47,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.1124,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.24,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 5.765,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": 0.02,
      "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": "ENST00000405093.9",
          "gene_symbol": "MYH6",
          "hgnc_id": 7576,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.3893C>T",
          "hgvs_p": "p.Ala1298Val"
        }
      ],
      "clinvar_disease": " susceptibility to,Atrial septal defect 3,Cardiovascular phenotype,Dilated cardiomyopathy 1EE,Hypertrophic cardiomyopathy 1,Hypertrophic cardiomyopathy 14,Long QT syndrome,Primary familial hypertrophic cardiomyopathy,Sick sinus syndrome 3,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:1 LB:4",
      "phenotype_combined": "Primary familial hypertrophic cardiomyopathy|Hypertrophic cardiomyopathy 14|not provided|Hypertrophic cardiomyopathy 14;Sick sinus syndrome 3, susceptibility to;Hypertrophic cardiomyopathy 1;Dilated cardiomyopathy 1EE;Atrial septal defect 3|Cardiovascular phenotype|Long QT syndrome",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}