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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: 11-119357286-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=119357286&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 119357286,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_004205.5",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP2",
"gene_hgnc_id": 12618,
"hgvs_c": "c.1631A>T",
"hgvs_p": "p.Tyr544Phe",
"transcript": "NM_004205.5",
"protein_id": "NP_004196.4",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 605,
"cds_start": 1631,
"cds_end": null,
"cds_length": 1818,
"cdna_start": 1890,
"cdna_end": null,
"cdna_length": 3697,
"mane_select": "ENST00000260187.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP2",
"gene_hgnc_id": 12618,
"hgvs_c": "c.1631A>T",
"hgvs_p": "p.Tyr544Phe",
"transcript": "ENST00000260187.7",
"protein_id": "ENSP00000260187.2",
"transcript_support_level": 1,
"aa_start": 544,
"aa_end": null,
"aa_length": 605,
"cds_start": 1631,
"cds_end": null,
"cds_length": 1818,
"cdna_start": 1890,
"cdna_end": null,
"cdna_length": 3697,
"mane_select": "NM_004205.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP2",
"gene_hgnc_id": 12618,
"hgvs_c": "c.1004A>T",
"hgvs_p": "p.Tyr335Phe",
"transcript": "ENST00000525735.1",
"protein_id": "ENSP00000436952.1",
"transcript_support_level": 1,
"aa_start": 335,
"aa_end": null,
"aa_length": 396,
"cds_start": 1004,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1216,
"cdna_end": null,
"cdna_length": 1704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP2",
"gene_hgnc_id": 12618,
"hgvs_c": "c.902A>T",
"hgvs_p": "p.Tyr301Phe",
"transcript": "ENST00000455332.6",
"protein_id": "ENSP00000407842.2",
"transcript_support_level": 1,
"aa_start": 301,
"aa_end": null,
"aa_length": 362,
"cds_start": 902,
"cds_end": null,
"cds_length": 1089,
"cdna_start": 1096,
"cdna_end": null,
"cdna_length": 2903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP2",
"gene_hgnc_id": 12618,
"hgvs_c": "c.1004A>T",
"hgvs_p": "p.Tyr335Phe",
"transcript": "NM_171997.3",
"protein_id": "NP_741994.1",
"transcript_support_level": null,
"aa_start": 335,
"aa_end": null,
"aa_length": 396,
"cds_start": 1004,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1217,
"cdna_end": null,
"cdna_length": 3024,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP2",
"gene_hgnc_id": 12618,
"hgvs_c": "c.902A>T",
"hgvs_p": "p.Tyr301Phe",
"transcript": "NM_001243759.2",
"protein_id": "NP_001230688.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 362,
"cds_start": 902,
"cds_end": null,
"cds_length": 1089,
"cdna_start": 1075,
"cdna_end": null,
"cdna_length": 2882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP2",
"gene_hgnc_id": 12618,
"hgvs_c": "c.1631A>T",
"hgvs_p": "p.Tyr544Phe",
"transcript": "XM_005271721.6",
"protein_id": "XP_005271778.1",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 605,
"cds_start": 1631,
"cds_end": null,
"cds_length": 1818,
"cdna_start": 1733,
"cdna_end": null,
"cdna_length": 3540,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP2",
"gene_hgnc_id": 12618,
"hgvs_c": "c.1631A>T",
"hgvs_p": "p.Tyr544Phe",
"transcript": "XM_005271722.3",
"protein_id": "XP_005271779.1",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 605,
"cds_start": 1631,
"cds_end": null,
"cds_length": 1818,
"cdna_start": 4516,
"cdna_end": null,
"cdna_length": 6323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP2",
"gene_hgnc_id": 12618,
"hgvs_c": "c.872A>T",
"hgvs_p": "p.Tyr291Phe",
"transcript": "XM_017018539.1",
"protein_id": "XP_016874028.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 352,
"cds_start": 872,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 887,
"cdna_end": null,
"cdna_length": 2694,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP2-AS1",
"gene_hgnc_id": 48673,
"hgvs_c": "n.251+569T>A",
"hgvs_p": null,
"transcript": "ENST00000706409.1",
"protein_id": null,
"transcript_support_level": null,
"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": 705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP2-AS1",
"gene_hgnc_id": 48673,
"hgvs_c": "n.238+569T>A",
"hgvs_p": null,
"transcript": "ENST00000844114.1",
"protein_id": null,
"transcript_support_level": null,
"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": 495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "USP2",
"gene_hgnc_id": 12618,
"dbsnp": "rs149898423",
"frequency_reference_population": 0.0011484835,
"hom_count_reference_population": 4,
"allele_count_reference_population": 1853,
"gnomad_exomes_af": 0.00115345,
"gnomad_genomes_af": 0.0011006,
"gnomad_exomes_ac": 1686,
"gnomad_genomes_ac": 167,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.027030736207962036,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.324,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1133,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.977,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_004205.5",
"gene_symbol": "USP2",
"hgnc_id": 12618,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1631A>T",
"hgvs_p": "p.Tyr544Phe"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000706409.1",
"gene_symbol": "USP2-AS1",
"hgnc_id": 48673,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.251+569T>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}