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: 8-96144995-C-G (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=96144995&ref=C&alt=G&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "8",
      "pos": 96144995,
      "ref": "C",
      "alt": "G",
      "effect": "synonymous_variant",
      "transcript": "ENST00000287020.7",
      "consequences": [
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_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.936G>C",
          "hgvs_p": "p.Ser312Ser",
          "transcript": "NM_001001557.4",
          "protein_id": "NP_001001557.1",
          "transcript_support_level": null,
          "aa_start": 312,
          "aa_end": null,
          "aa_length": 455,
          "cds_start": 936,
          "cds_end": null,
          "cds_length": 1368,
          "cdna_start": 1050,
          "cdna_end": null,
          "cdna_length": 3712,
          "mane_select": "ENST00000287020.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_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.936G>C",
          "hgvs_p": "p.Ser312Ser",
          "transcript": "ENST00000287020.7",
          "protein_id": "ENSP00000287020.4",
          "transcript_support_level": 1,
          "aa_start": 312,
          "aa_end": null,
          "aa_length": 455,
          "cds_start": 936,
          "cds_end": null,
          "cds_length": 1368,
          "cdna_start": 1050,
          "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": "rs148861809",
      "frequency_reference_population": 0.03628723,
      "hom_count_reference_population": 1047,
      "allele_count_reference_population": 50066,
      "gnomad_exomes_af": 0.0375276,
      "gnomad_genomes_af": 0.0262033,
      "gnomad_exomes_ac": 46106,
      "gnomad_genomes_ac": 3960,
      "gnomad_exomes_homalt": 965,
      "gnomad_genomes_homalt": 82,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.8399999737739563,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.84,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -2.179,
      "phylop100way_prediction": "Benign",
      "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": -21,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
      "acmg_by_gene": [
        {
          "score": -21,
          "benign_score": 21,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BP7",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000287020.7",
          "gene_symbol": "GDF6",
          "hgnc_id": 4221,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AD,Unknown",
          "hgvs_c": "c.936G>C",
          "hgvs_p": "p.Ser312Ser"
        }
      ],
      "clinvar_disease": " autosomal dominant, isolated, with coloboma 6,Isolated microphthalmia 4,Klippel-Feil syndrome 1,Leber congenital amaurosis 17,Microphthalmia,not provided,not specified",
      "clinvar_classification": "Benign/Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:2 B:3",
      "phenotype_combined": "not specified|Klippel-Feil syndrome 1, autosomal dominant|Isolated microphthalmia 4;Leber congenital amaurosis 17;Klippel-Feil syndrome 1, autosomal dominant;Microphthalmia, isolated, with coloboma 6|not provided",
      "pathogenicity_classification_combined": "Benign/Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}