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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-12842411-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=Y&pos=12842411&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "Y",
"pos": 12842411,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_004654.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.6384C>T",
"hgvs_p": "p.Ser2128Ser",
"transcript": "NM_004654.4",
"protein_id": "NP_004645.2",
"transcript_support_level": null,
"aa_start": 2128,
"aa_end": null,
"aa_length": 2555,
"cds_start": 6384,
"cds_end": null,
"cds_length": 7668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000338981.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004654.4"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.6384C>T",
"hgvs_p": "p.Ser2128Ser",
"transcript": "ENST00000338981.7",
"protein_id": "ENSP00000342812.3",
"transcript_support_level": 1,
"aa_start": 2128,
"aa_end": null,
"aa_length": 2555,
"cds_start": 6384,
"cds_end": null,
"cds_length": 7668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004654.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000338981.7"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.6384C>T",
"hgvs_p": "p.Ser2128Ser",
"transcript": "ENST00000651177.1",
"protein_id": "ENSP00000498372.1",
"transcript_support_level": null,
"aa_start": 2128,
"aa_end": null,
"aa_length": 2555,
"cds_start": 6384,
"cds_end": null,
"cds_length": 7668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000651177.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.6384C>T",
"hgvs_p": "p.Ser2128Ser",
"transcript": "ENST00000857541.1",
"protein_id": "ENSP00000527600.1",
"transcript_support_level": null,
"aa_start": 2128,
"aa_end": null,
"aa_length": 2555,
"cds_start": 6384,
"cds_end": null,
"cds_length": 7668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857541.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.6384C>T",
"hgvs_p": "p.Ser2128Ser",
"transcript": "ENST00000932611.1",
"protein_id": "ENSP00000602670.1",
"transcript_support_level": null,
"aa_start": 2128,
"aa_end": null,
"aa_length": 2555,
"cds_start": 6384,
"cds_end": null,
"cds_length": 7668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932611.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.6384C>T",
"hgvs_p": "p.Ser2128Ser",
"transcript": "ENST00000932612.1",
"protein_id": "ENSP00000602671.1",
"transcript_support_level": null,
"aa_start": 2128,
"aa_end": null,
"aa_length": 2555,
"cds_start": 6384,
"cds_end": null,
"cds_length": 7668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932612.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.6384C>T",
"hgvs_p": "p.Ser2128Ser",
"transcript": "ENST00000932615.1",
"protein_id": "ENSP00000602674.1",
"transcript_support_level": null,
"aa_start": 2128,
"aa_end": null,
"aa_length": 2555,
"cds_start": 6384,
"cds_end": null,
"cds_length": 7668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932615.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.6384C>T",
"hgvs_p": "p.Ser2128Ser",
"transcript": "ENST00000942408.1",
"protein_id": "ENSP00000612467.1",
"transcript_support_level": null,
"aa_start": 2128,
"aa_end": null,
"aa_length": 2548,
"cds_start": 6384,
"cds_end": null,
"cds_length": 7647,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942408.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.6384C>T",
"hgvs_p": "p.Ser2128Ser",
"transcript": "ENST00000932614.1",
"protein_id": "ENSP00000602673.1",
"transcript_support_level": null,
"aa_start": 2128,
"aa_end": null,
"aa_length": 2530,
"cds_start": 6384,
"cds_end": null,
"cds_length": 7593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932614.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.5925C>T",
"hgvs_p": "p.Ser1975Ser",
"transcript": "ENST00000932613.1",
"protein_id": "ENSP00000602672.1",
"transcript_support_level": null,
"aa_start": 1975,
"aa_end": null,
"aa_length": 2402,
"cds_start": 5925,
"cds_end": null,
"cds_length": 7209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932613.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.6384C>T",
"hgvs_p": "p.Ser2128Ser",
"transcript": "XM_047442772.1",
"protein_id": "XP_047298728.1",
"transcript_support_level": null,
"aa_start": 2128,
"aa_end": null,
"aa_length": 2555,
"cds_start": 6384,
"cds_end": null,
"cds_length": 7668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442772.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.6150C>T",
"hgvs_p": "p.Ser2050Ser",
"transcript": "XM_047442771.1",
"protein_id": "XP_047298727.1",
"transcript_support_level": null,
"aa_start": 2050,
"aa_end": null,
"aa_length": 2477,
"cds_start": 6150,
"cds_end": null,
"cds_length": 7434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442771.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": 41,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "c.6252+132C>T",
"hgvs_p": null,
"transcript": "ENST00000932610.1",
"protein_id": "ENSP00000602669.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2468,
"cds_start": null,
"cds_end": null,
"cds_length": 7407,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932610.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"hgvs_c": "n.6411C>T",
"hgvs_p": null,
"transcript": "ENST00000426564.6",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000426564.6"
}
],
"gene_symbol": "USP9Y",
"gene_hgnc_id": 12633,
"dbsnp": "rs200311491",
"frequency_reference_population": 0.00006190034,
"hom_count_reference_population": 2,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.000121185,
"gnomad_genomes_af": 0.0000619003,
"gnomad_exomes_ac": 44,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5400000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.031,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.1,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7,BS2",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_004654.4",
"gene_symbol": "USP9Y",
"hgnc_id": 12633,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "YL",
"hgvs_c": "c.6384C>T",
"hgvs_p": "p.Ser2128Ser"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}