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: 14-23387778-C-T (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=23387778&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "14",
      "pos": 23387778,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000405093.9",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "Q",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 31,
          "exon_rank_end": null,
          "exon_count": 39,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYH6",
          "gene_hgnc_id": 7576,
          "hgvs_c": "c.4505G>A",
          "hgvs_p": "p.Arg1502Gln",
          "transcript": "NM_002471.4",
          "protein_id": "NP_002462.2",
          "transcript_support_level": null,
          "aa_start": 1502,
          "aa_end": null,
          "aa_length": 1939,
          "cds_start": 4505,
          "cds_end": null,
          "cds_length": 5820,
          "cdna_start": 4572,
          "cdna_end": null,
          "cdna_length": 5940,
          "mane_select": "ENST00000405093.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "Q",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 31,
          "exon_rank_end": null,
          "exon_count": 39,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYH6",
          "gene_hgnc_id": 7576,
          "hgvs_c": "c.4505G>A",
          "hgvs_p": "p.Arg1502Gln",
          "transcript": "ENST00000405093.9",
          "protein_id": "ENSP00000386041.3",
          "transcript_support_level": 5,
          "aa_start": 1502,
          "aa_end": null,
          "aa_length": 1939,
          "cds_start": 4505,
          "cds_end": null,
          "cds_length": 5820,
          "cdna_start": 4572,
          "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": "rs199936506",
      "frequency_reference_population": 0.00017534794,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 283,
      "gnomad_exomes_af": 0.000171011,
      "gnomad_genomes_af": 0.000217048,
      "gnomad_exomes_ac": 250,
      "gnomad_genomes_ac": 33,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.5063328742980957,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.831,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.4292,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.19,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 7.624,
      "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": -5,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP6,BS2",
      "acmg_by_gene": [
        {
          "score": -5,
          "benign_score": 5,
          "pathogenic_score": 0,
          "criteria": [
            "BP6",
            "BS2"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000405093.9",
          "gene_symbol": "MYH6",
          "hgnc_id": 7576,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.4505G>A",
          "hgvs_p": "p.Arg1502Gln"
        }
      ],
      "clinvar_disease": " susceptibility to,Atrial septal defect 3,Cardiovascular phenotype,Dilated cardiomyopathy 1EE,Hypertrophic cardiomyopathy 1,Hypertrophic cardiomyopathy 14,MYH6-related disorder,Primary dilated cardiomyopathy,Primary familial dilated cardiomyopathy,Sick sinus syndrome 3,not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:6 LB:3",
      "phenotype_combined": "not specified|Primary dilated cardiomyopathy|Hypertrophic cardiomyopathy 14|Primary familial dilated cardiomyopathy|Atrial septal defect 3;Hypertrophic cardiomyopathy 1;Dilated cardiomyopathy 1EE;Hypertrophic cardiomyopathy 14;Sick sinus syndrome 3, susceptibility to|not provided|MYH6-related disorder|Cardiovascular phenotype",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}