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: M-11778-G-A (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=M&pos=11778&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "M",
      "pos": 11778,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "ENST00000361381.2",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 1,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MT-ND4",
          "gene_hgnc_id": 7459,
          "hgvs_c": "c.1019G>A",
          "hgvs_p": "p.Arg340His",
          "transcript": "ENST00000361381.2",
          "protein_id": "ENSP00000354961.2",
          "transcript_support_level": 6,
          "aa_start": 340,
          "aa_end": null,
          "aa_length": 458,
          "cds_start": 1019,
          "cds_end": null,
          "cds_length": 1378,
          "cdna_start": 1019,
          "cdna_end": null,
          "cdna_length": 1378,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": null,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 1,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ND4",
          "gene_hgnc_id": 7459,
          "hgvs_c": "c.1019G>A",
          "hgvs_p": "p.Arg340His",
          "transcript": "unassigned_transcript_4811",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": 340,
          "aa_end": null,
          "aa_length": 458,
          "cds_start": 1019,
          "cds_end": null,
          "cds_length": 1378,
          "cdna_start": 1019,
          "cdna_end": null,
          "cdna_length": 1378,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "MT-ND4",
      "gene_hgnc_id": 7459,
      "dbsnp": "rs199476112",
      "frequency_reference_population": null,
      "hom_count_reference_population": 11,
      "allele_count_reference_population": 11,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": 11,
      "gnomad_mito_heteroplasmic": 13,
      "computational_score_selected": 0.9260421991348267,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "Apogee2",
      "splice_score_selected": null,
      "splice_prediction_selected": null,
      "splice_source_selected": null,
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": 0.8615,
      "alphamissense_prediction": "Pathogenic",
      "bayesdelnoaf_score": null,
      "bayesdelnoaf_prediction": null,
      "phylop100way_score": 3.757,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": null,
      "spliceai_max_prediction": null,
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": 0.9260421991348267,
      "apogee2_prediction": "Pathogenic",
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": 8,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PS4,PP1_Moderate,PS3_Supporting,PP3",
      "acmg_by_gene": [
        {
          "score": 8,
          "benign_score": 0,
          "pathogenic_score": 8,
          "criteria": [
            "PS4",
            "PP1_Moderate",
            "PS3_Supporting",
            "PP3"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000361381.2",
          "gene_symbol": "MT-ND4",
          "hgnc_id": 7459,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "Mitochondrial",
          "hgvs_c": "c.1019G>A",
          "hgvs_p": "p.Arg340His"
        },
        {
          "score": 8,
          "benign_score": 0,
          "pathogenic_score": 8,
          "criteria": [
            "PS4",
            "PP1_Moderate",
            "PS3_Supporting",
            "PP3"
          ],
          "verdict": "Pathogenic",
          "transcript": "unassigned_transcript_4811",
          "gene_symbol": "ND4",
          "hgnc_id": 7459,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "Mitochondrial",
          "hgvs_c": "c.1019G>A",
          "hgvs_p": "p.Arg340His"
        }
      ],
      "clinvar_disease": " susceptibility to,Leber optic atrophy,Leber optic atrophy and dystonia,Mitochondrial disease,Optic atrophy,Retinal dystrophy,not provided,not specified",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "reviewed by expert panel",
      "clinvar_submissions_summary": "P:15 O:2",
      "phenotype_combined": "LHON-/-Progressive-Dystonia,Leber optic atrophy|not provided|Mitochondrial disease|not specified|Leber optic atrophy and dystonia|Leber optic atrophy, susceptibility to|Optic atrophy|Retinal dystrophy",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}