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: 6-42698407-C-T (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=42698407&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "6",
      "pos": 42698407,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000230381.7",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRPH2",
          "gene_hgnc_id": 9942,
          "hgvs_c": "c.929G>A",
          "hgvs_p": "p.Arg310Lys",
          "transcript": "NM_000322.5",
          "protein_id": "NP_000313.2",
          "transcript_support_level": null,
          "aa_start": 310,
          "aa_end": null,
          "aa_length": 346,
          "cds_start": 929,
          "cds_end": null,
          "cds_length": 1041,
          "cdna_start": 1192,
          "cdna_end": null,
          "cdna_length": 3001,
          "mane_select": "ENST00000230381.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PRPH2",
          "gene_hgnc_id": 9942,
          "hgvs_c": "c.929G>A",
          "hgvs_p": "p.Arg310Lys",
          "transcript": "ENST00000230381.7",
          "protein_id": "ENSP00000230381.5",
          "transcript_support_level": 1,
          "aa_start": 310,
          "aa_end": null,
          "aa_length": 346,
          "cds_start": 929,
          "cds_end": null,
          "cds_length": 1041,
          "cdna_start": 1192,
          "cdna_end": null,
          "cdna_length": 3001,
          "mane_select": "NM_000322.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "PRPH2",
      "gene_hgnc_id": 9942,
      "dbsnp": "rs425876",
      "frequency_reference_population": 0.9051395,
      "hom_count_reference_population": 662152,
      "allele_count_reference_population": 1461002,
      "gnomad_exomes_af": 0.902873,
      "gnomad_genomes_af": 0.926901,
      "gnomad_exomes_ac": 1319885,
      "gnomad_genomes_ac": 141117,
      "gnomad_exomes_homalt": 596602,
      "gnomad_genomes_homalt": 65550,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 6.280707793848705e-7,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.177,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0551,
      "alphamissense_prediction": "Benign",
      "bayesdelnoaf_score": -0.63,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 2.847,
      "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": -17,
      "acmg_classification": "Benign",
      "acmg_criteria": "PM1,PP2,BP4_Strong,BP6_Very_Strong,BA1",
      "acmg_by_gene": [
        {
          "score": -17,
          "benign_score": 20,
          "pathogenic_score": 3,
          "criteria": [
            "PM1",
            "PP2",
            "BP4_Strong",
            "BP6_Very_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000230381.7",
          "gene_symbol": "PRPH2",
          "hgnc_id": 9942,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "SD,AD,AR",
          "hgvs_c": "c.929G>A",
          "hgvs_p": "p.Arg310Lys"
        }
      ],
      "clinvar_disease": " central areolar 2,Adult-onset foveomacular vitelliform dystrophy,Choroidal dystrophy,Cone-rod dystrophy,PRPH2-related disorder,Patterned macular dystrophy 1,Pigmentary retinal dystrophy,Retinal dystrophy,Retinitis pigmentosa,Retinitis pigmentosa 7,Vitelliform macular dystrophy 3,not provided,not specified",
      "clinvar_classification": "Benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "B:18",
      "phenotype_combined": "not specified|Choroidal dystrophy, central areolar 2|Cone-rod dystrophy|Retinitis pigmentosa|PRPH2-related disorder|Retinitis pigmentosa 7|Vitelliform macular dystrophy 3|not provided|Patterned macular dystrophy 1|Pigmentary retinal dystrophy|Retinal dystrophy|Adult-onset foveomacular vitelliform dystrophy",
      "pathogenicity_classification_combined": "Benign",
      "custom_annotations": null
    }
  ],
  "message": null
}