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: 8-96144660-T-C (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=96144660&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "8",
      "pos": 96144660,
      "ref": "T",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "ENST00000287020.7",
      "consequences": [
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GDF6",
          "gene_hgnc_id": 4221,
          "hgvs_c": "c.1271A>G",
          "hgvs_p": "p.Lys424Arg",
          "transcript": "NM_001001557.4",
          "protein_id": "NP_001001557.1",
          "transcript_support_level": null,
          "aa_start": 424,
          "aa_end": null,
          "aa_length": 455,
          "cds_start": 1271,
          "cds_end": null,
          "cds_length": 1368,
          "cdna_start": 1385,
          "cdna_end": null,
          "cdna_length": 3712,
          "mane_select": "ENST00000287020.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GDF6",
          "gene_hgnc_id": 4221,
          "hgvs_c": "c.1271A>G",
          "hgvs_p": "p.Lys424Arg",
          "transcript": "ENST00000287020.7",
          "protein_id": "ENSP00000287020.4",
          "transcript_support_level": 1,
          "aa_start": 424,
          "aa_end": null,
          "aa_length": 455,
          "cds_start": 1271,
          "cds_end": null,
          "cds_length": 1368,
          "cdna_start": 1385,
          "cdna_end": null,
          "cdna_length": 3712,
          "mane_select": "NM_001001557.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "GDF6",
      "gene_hgnc_id": 4221,
      "dbsnp": "rs121909353",
      "frequency_reference_population": 0.00006938998,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 112,
      "gnomad_exomes_af": 0.0000697744,
      "gnomad_genomes_af": 0.0000656978,
      "gnomad_exomes_ac": 102,
      "gnomad_genomes_ac": 10,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.017830073833465576,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.573,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.0911,
      "alphamissense_prediction": "Benign",
      "bayesdelnoaf_score": -0.02,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 4.216,
      "phylop100way_prediction": "Uncertain_significance",
      "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": -9,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6,BS2",
      "acmg_by_gene": [
        {
          "score": -9,
          "benign_score": 9,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000287020.7",
          "gene_symbol": "GDF6",
          "hgnc_id": 4221,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,Unknown",
          "hgvs_c": "c.1271A>G",
          "hgvs_p": "p.Lys424Arg"
        }
      ],
      "clinvar_disease": " autosomal dominant, isolated, with coloboma 6,Autosomal dominant Parkinson disease 8,Isolated microphthalmia 4,Klippel-Feil syndrome,Klippel-Feil syndrome 1,Leber congenital amaurosis 17,Microphthalmia,Multiple synostoses syndrome 4",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:2 LB:2",
      "phenotype_combined": "Klippel-Feil syndrome 1, autosomal dominant|Klippel-Feil syndrome|Klippel-Feil syndrome 1, autosomal dominant;Autosomal dominant Parkinson disease 8|Klippel-Feil syndrome 1, autosomal dominant;Isolated microphthalmia 4;Microphthalmia, isolated, with coloboma 6;Leber congenital amaurosis 17|Leber congenital amaurosis 17|Klippel-Feil syndrome 1, autosomal dominant;Isolated microphthalmia 4;Multiple synostoses syndrome 4;Microphthalmia, isolated, with coloboma 6;Leber congenital amaurosis 17",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}