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: 1-114713909-G-T (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=114713909&ref=G&alt=T&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "1",
      "pos": 114713909,
      "ref": "G",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000369535.5",
      "consequences": [
        {
          "aa_ref": "Q",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NRAS",
          "gene_hgnc_id": 7989,
          "hgvs_c": "c.181C>A",
          "hgvs_p": "p.Gln61Lys",
          "transcript": "NM_002524.5",
          "protein_id": "NP_002515.1",
          "transcript_support_level": null,
          "aa_start": 61,
          "aa_end": null,
          "aa_length": 189,
          "cds_start": 181,
          "cds_end": null,
          "cds_length": 570,
          "cdna_start": 312,
          "cdna_end": null,
          "cdna_length": 4326,
          "mane_select": "ENST00000369535.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "K",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NRAS",
          "gene_hgnc_id": 7989,
          "hgvs_c": "c.181C>A",
          "hgvs_p": "p.Gln61Lys",
          "transcript": "ENST00000369535.5",
          "protein_id": "ENSP00000358548.4",
          "transcript_support_level": 1,
          "aa_start": 61,
          "aa_end": null,
          "aa_length": 189,
          "cds_start": 181,
          "cds_end": null,
          "cds_length": 570,
          "cdna_start": 312,
          "cdna_end": null,
          "cdna_length": 4326,
          "mane_select": "NM_002524.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "NRAS",
      "gene_hgnc_id": 7989,
      "dbsnp": "rs121913254",
      "frequency_reference_population": 6.8486304e-7,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 1,
      "gnomad_exomes_af": 6.84863e-7,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 1,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.8959176540374756,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.841,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9853,
      "alphamissense_prediction": "Pathogenic",
      "bayesdelnoaf_score": 0.36,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 9.865,
      "phylop100way_prediction": "Pathogenic",
      "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": 10,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Moderate,PP5",
      "acmg_by_gene": [
        {
          "score": 10,
          "benign_score": 0,
          "pathogenic_score": 10,
          "criteria": [
            "PM1",
            "PM2",
            "PM5",
            "PP2",
            "PP3_Moderate",
            "PP5"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000369535.5",
          "gene_symbol": "NRAS",
          "hgnc_id": 7989,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.181C>A",
          "hgvs_p": "p.Gln61Lys"
        }
      ],
      "clinvar_disease": "Colorectal cancer,Epidermal nevus,Large congenital melanocytic nevus,Neoplasm,Neurocutaneous melanocytosis,RASopathy,Ras Inhibitor response,Vascular Tumors Including Pyogenic Granuloma,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "P:3 LP:1 US:2",
      "phenotype_combined": "Neurocutaneous melanocytosis|Large congenital melanocytic nevus|Vascular Tumors Including Pyogenic Granuloma|not provided|Ras Inhibitor response|RASopathy|Neoplasm|Colorectal cancer|Large congenital melanocytic nevus;Epidermal nevus",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}