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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: 10-69266754-C-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=69266754&ref=C&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "10",
      "pos": 69266754,
      "ref": "C",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "ENST00000354624.6",
      "consequences": [
        {
          "aa_ref": "N",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HKDC1",
          "gene_hgnc_id": 23302,
          "hgvs_c": "c.2751C>A",
          "hgvs_p": "p.Asn917Lys",
          "transcript": "NM_025130.4",
          "protein_id": "NP_079406.4",
          "transcript_support_level": null,
          "aa_start": 917,
          "aa_end": null,
          "aa_length": 917,
          "cds_start": 2751,
          "cds_end": null,
          "cds_length": 2754,
          "cdna_start": 2855,
          "cdna_end": null,
          "cdna_length": 3653,
          "mane_select": "ENST00000354624.6",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "K",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HKDC1",
          "gene_hgnc_id": 23302,
          "hgvs_c": "c.2751C>A",
          "hgvs_p": "p.Asn917Lys",
          "transcript": "ENST00000354624.6",
          "protein_id": "ENSP00000346643.5",
          "transcript_support_level": 1,
          "aa_start": 917,
          "aa_end": null,
          "aa_length": 917,
          "cds_start": 2751,
          "cds_end": null,
          "cds_length": 2754,
          "cdna_start": 2855,
          "cdna_end": null,
          "cdna_length": 3653,
          "mane_select": "NM_025130.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HKDC1",
          "gene_hgnc_id": 23302,
          "hgvs_c": "c.2175C>A",
          "hgvs_p": "p.Asn725Lys",
          "transcript": "XM_047425784.1",
          "protein_id": "XP_047281740.1",
          "transcript_support_level": null,
          "aa_start": 725,
          "aa_end": null,
          "aa_length": 725,
          "cds_start": 2175,
          "cds_end": null,
          "cds_length": 2178,
          "cdna_start": 4165,
          "cdna_end": null,
          "cdna_length": 4963,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000231748",
          "gene_hgnc_id": null,
          "hgvs_c": "n.49-1027G>T",
          "hgvs_p": null,
          "transcript": "ENST00000413220.1",
          "protein_id": null,
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 434,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "HKDC1",
      "gene_hgnc_id": 23302,
      "dbsnp": "rs906219",
      "frequency_reference_population": 0.33280826,
      "hom_count_reference_population": 93669,
      "allele_count_reference_population": 535790,
      "gnomad_exomes_af": 0.336203,
      "gnomad_genomes_af": 0.300259,
      "gnomad_exomes_ac": 490135,
      "gnomad_genomes_ac": 45655,
      "gnomad_exomes_homalt": 85883,
      "gnomad_genomes_homalt": 7786,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.0001647472381591797,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.24,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.091,
      "alphamissense_prediction": "Benign",
      "bayesdelnoaf_score": -0.25,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 1.189,
      "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": -12,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BA1",
      "acmg_by_gene": [
        {
          "score": -12,
          "benign_score": 12,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000354624.6",
          "gene_symbol": "HKDC1",
          "hgnc_id": 23302,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.2751C>A",
          "hgvs_p": "p.Asn917Lys"
        },
        {
          "score": -12,
          "benign_score": 12,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000413220.1",
          "gene_symbol": "ENSG00000231748",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.49-1027G>T",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "",
      "clinvar_classification": "",
      "clinvar_review_status": "",
      "clinvar_submissions_summary": "",
      "phenotype_combined": null,
      "pathogenicity_classification_combined": null,
      "custom_annotations": null
    }
  ],
  "message": null
}