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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: Y-12739604-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=Y&pos=12739604&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "Y",
"pos": 12739604,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000338981.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.1397T>A",
"hgvs_p": "p.Leu466His",
"transcript": "NM_004654.4",
"protein_id": "NP_004645.2",
"transcript_support_level": null,
"aa_start": 466,
"aa_end": null,
"aa_length": 2555,
"cds_start": 1397,
"cds_end": null,
"cds_length": 7668,
"cdna_start": 2342,
"cdna_end": null,
"cdna_length": 10036,
"mane_select": "ENST00000338981.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.1397T>A",
"hgvs_p": "p.Leu466His",
"transcript": "ENST00000338981.7",
"protein_id": "ENSP00000342812.3",
"transcript_support_level": 1,
"aa_start": 466,
"aa_end": null,
"aa_length": 2555,
"cds_start": 1397,
"cds_end": null,
"cds_length": 7668,
"cdna_start": 2342,
"cdna_end": null,
"cdna_length": 10036,
"mane_select": "NM_004654.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.1397T>A",
"hgvs_p": "p.Leu466His",
"transcript": "ENST00000651177.1",
"protein_id": "ENSP00000498372.1",
"transcript_support_level": null,
"aa_start": 466,
"aa_end": null,
"aa_length": 2555,
"cds_start": 1397,
"cds_end": null,
"cds_length": 7668,
"cdna_start": 1983,
"cdna_end": null,
"cdna_length": 9640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.1397T>A",
"hgvs_p": "p.Leu466His",
"transcript": "XM_047442772.1",
"protein_id": "XP_047298728.1",
"transcript_support_level": null,
"aa_start": 466,
"aa_end": null,
"aa_length": 2555,
"cds_start": 1397,
"cds_end": null,
"cds_length": 7668,
"cdna_start": 1546,
"cdna_end": null,
"cdna_length": 9240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.1163T>A",
"hgvs_p": "p.Leu388His",
"transcript": "XM_047442771.1",
"protein_id": "XP_047298727.1",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 2477,
"cds_start": 1163,
"cds_end": null,
"cds_length": 7434,
"cdna_start": 1540,
"cdna_end": null,
"cdna_length": 9234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "n.1409T>A",
"hgvs_p": null,
"transcript": "ENST00000426564.6",
"protein_id": null,
"transcript_support_level": 2,
"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": 9118,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"dbsnp": "rs3212292",
"frequency_reference_population": 0.00014751873,
"hom_count_reference_population": 5,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.0000195278,
"gnomad_genomes_af": 0.000147519,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8070738315582275,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.8942,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.12,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.52,
"phylop100way_prediction": "Uncertain_significance",
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000338981.7",
"gene_symbol": "USP9Y",
"hgnc_id": 12633,
"effects": [
"missense_variant"
],
"inheritance_mode": "YL",
"hgvs_c": "c.1397T>A",
"hgvs_p": "p.Leu466His"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}