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: 2-21008652-G-A (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=21008652&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "2",
      "pos": 21008652,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_000384.3",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 26,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APOB",
          "gene_hgnc_id": 603,
          "hgvs_c": "c.8216C>T",
          "hgvs_p": "p.Pro2739Leu",
          "transcript": "NM_000384.3",
          "protein_id": "NP_000375.3",
          "transcript_support_level": null,
          "aa_start": 2739,
          "aa_end": null,
          "aa_length": 4563,
          "cds_start": 8216,
          "cds_end": null,
          "cds_length": 13692,
          "cdna_start": 8344,
          "cdna_end": null,
          "cdna_length": 14121,
          "mane_select": "ENST00000233242.5",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_000384.3"
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 26,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APOB",
          "gene_hgnc_id": 603,
          "hgvs_c": "c.8216C>T",
          "hgvs_p": "p.Pro2739Leu",
          "transcript": "ENST00000233242.5",
          "protein_id": "ENSP00000233242.1",
          "transcript_support_level": 1,
          "aa_start": 2739,
          "aa_end": null,
          "aa_length": 4563,
          "cds_start": 8216,
          "cds_end": null,
          "cds_length": 13692,
          "cdna_start": 8344,
          "cdna_end": null,
          "cdna_length": 14121,
          "mane_select": "NM_000384.3",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000233242.5"
        }
      ],
      "gene_symbol": "APOB",
      "gene_hgnc_id": 603,
      "dbsnp": "rs676210",
      "frequency_reference_population": 0.24208216,
      "hom_count_reference_population": 57804,
      "allele_count_reference_population": 390663,
      "gnomad_exomes_af": 0.243351,
      "gnomad_genomes_af": 0.229884,
      "gnomad_exomes_ac": 355716,
      "gnomad_genomes_ac": 34947,
      "gnomad_exomes_homalt": 52727,
      "gnomad_genomes_homalt": 5077,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.00002933530049631372,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.373,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.2498,
      "alphamissense_prediction": "Benign",
      "bayesdelnoaf_score": -0.41,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 10.003,
      "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": -20,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
      "acmg_by_gene": [
        {
          "score": -20,
          "benign_score": 20,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "NM_000384.3",
          "gene_symbol": "APOB",
          "hgnc_id": 603,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR,SD",
          "hgvs_c": "c.8216C>T",
          "hgvs_p": "p.Pro2739Leu"
        }
      ],
      "clinvar_disease": " 1, autosomal dominant, familial, type B,Cardiovascular phenotype,Familial hypercholesterolemia,Familial hypobetalipoproteinemia 1,Hypercholesterolemia,Isolated systolic hypertension,Neutrophilia in presence of infection,Triangular shaped proximal phalanx of the thumb,not provided,not specified",
      "clinvar_classification": "Benign/Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:3 B:10",
      "phenotype_combined": "not specified|Hypercholesterolemia, familial, 1|Familial hypobetalipoproteinemia 1|Familial hypobetalipoproteinemia 1;Hypercholesterolemia, autosomal dominant, type B|Familial hypercholesterolemia|Hypercholesterolemia, autosomal dominant, type B|Cardiovascular phenotype|Triangular shaped proximal phalanx of the thumb;Neutrophilia in presence of infection;Isolated systolic hypertension|not provided",
      "pathogenicity_classification_combined": "Benign/Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}