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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: 17-4933119-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=4933119&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 4933119,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000329125.6",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GP1BA",
"gene_hgnc_id": 4439,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ala172Val",
"transcript": "NM_000173.7",
"protein_id": "NP_000164.5",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 652,
"cds_start": 515,
"cds_end": null,
"cds_length": 1959,
"cdna_start": 610,
"cdna_end": null,
"cdna_length": 2514,
"mane_select": "ENST00000329125.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GP1BA",
"gene_hgnc_id": 4439,
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ala172Val",
"transcript": "ENST00000329125.6",
"protein_id": "ENSP00000329380.5",
"transcript_support_level": 1,
"aa_start": 172,
"aa_end": null,
"aa_length": 652,
"cds_start": 515,
"cds_end": null,
"cds_length": 1959,
"cdna_start": 610,
"cdna_end": null,
"cdna_length": 2514,
"mane_select": "NM_000173.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CHRNE",
"gene_hgnc_id": 1966,
"hgvs_c": "c.-888+1223G>A",
"hgvs_p": null,
"transcript": "ENST00000649830.1",
"protein_id": "ENSP00000496907.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 179,
"cds_start": -4,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2293,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GP1BA",
"gene_hgnc_id": 4439,
"dbsnp": "rs121908065",
"frequency_reference_population": 0.0000013684103,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136841,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5952646136283875,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.359,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7713,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.09,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.982,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000329125.6",
"gene_symbol": "GP1BA",
"hgnc_id": 4439,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Ala172Val"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000649830.1",
"gene_symbol": "CHRNE",
"hgnc_id": 1966,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.-888+1223G>A",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal dominant, susceptibility to, type A1, type A2,Bernard Soulier syndrome,Bernard-Soulier syndrome,Nonarteritic anterior ischemic optic neuropathy,Pseudo von Willebrand disease,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4",
"phenotype_combined": "Bernard-Soulier syndrome, type A1|Bernard-Soulier syndrome, type A2, autosomal dominant|not provided|Pseudo von Willebrand disease;Bernard-Soulier syndrome, type A2, autosomal dominant;Nonarteritic anterior ischemic optic neuropathy, susceptibility to;Bernard Soulier syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}