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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: 10-53806693-G-GTCAA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=53806693&ref=G&alt=GTCAA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 53806693,
"ref": "G",
"alt": "GTCAA",
"effect": "frameshift_variant,stop_gained",
"transcript": "ENST00000644397.2",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.5105_5108dupTTGA",
"hgvs_p": "p.Ser1704fs",
"transcript": "NM_001384140.1",
"protein_id": "NP_001371069.1",
"transcript_support_level": null,
"aa_start": 1703,
"aa_end": null,
"aa_length": 1740,
"cds_start": 5108,
"cds_end": null,
"cds_length": 5223,
"cdna_start": 5443,
"cdna_end": null,
"cdna_length": 9366,
"mane_select": "ENST00000644397.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.5105_5108dupTTGA",
"hgvs_p": "p.Ser1704fs",
"transcript": "ENST00000644397.2",
"protein_id": "ENSP00000495195.1",
"transcript_support_level": null,
"aa_start": 1703,
"aa_end": null,
"aa_length": 1740,
"cds_start": 5108,
"cds_end": null,
"cds_length": 5223,
"cdna_start": 5443,
"cdna_end": null,
"cdna_length": 9366,
"mane_select": "NM_001384140.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.4910_4913dupTTGA",
"hgvs_p": "p.Ser1639fs",
"transcript": "ENST00000616114.4",
"protein_id": "ENSP00000483745.1",
"transcript_support_level": 1,
"aa_start": 1638,
"aa_end": null,
"aa_length": 1675,
"cds_start": 4913,
"cds_end": null,
"cds_length": 5028,
"cdna_start": 5308,
"cdna_end": null,
"cdna_length": 5846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.5039_5042dupTTGA",
"hgvs_p": "p.Ser1682fs",
"transcript": "NM_001354429.2",
"protein_id": "NP_001341358.1",
"transcript_support_level": null,
"aa_start": 1681,
"aa_end": null,
"aa_length": 1718,
"cds_start": 5042,
"cds_end": null,
"cds_length": 5157,
"cdna_start": 5377,
"cdna_end": null,
"cdna_length": 9300,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.4931_4934dupTTGA",
"hgvs_p": "p.Ser1646fs",
"transcript": "NM_001142771.2",
"protein_id": "NP_001136243.1",
"transcript_support_level": null,
"aa_start": 1645,
"aa_end": null,
"aa_length": 1682,
"cds_start": 4934,
"cds_end": null,
"cds_length": 5049,
"cdna_start": 5269,
"cdna_end": null,
"cdna_length": 9192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.4931_4934dupTTGA",
"hgvs_p": "p.Ser1646fs",
"transcript": "ENST00000621708.4",
"protein_id": "ENSP00000484454.1",
"transcript_support_level": 5,
"aa_start": 1645,
"aa_end": null,
"aa_length": 1682,
"cds_start": 4934,
"cds_end": null,
"cds_length": 5049,
"cdna_start": 5329,
"cdna_end": null,
"cdna_length": 5700,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.4916_4919dupTTGA",
"hgvs_p": "p.Ser1641fs",
"transcript": "NM_001142772.2",
"protein_id": "NP_001136244.1",
"transcript_support_level": null,
"aa_start": 1640,
"aa_end": null,
"aa_length": 1677,
"cds_start": 4919,
"cds_end": null,
"cds_length": 5034,
"cdna_start": 5254,
"cdna_end": null,
"cdna_length": 9177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.4916_4919dupTTGA",
"hgvs_p": "p.Ser1641fs",
"transcript": "ENST00000373965.6",
"protein_id": "ENSP00000363076.3",
"transcript_support_level": 5,
"aa_start": 1640,
"aa_end": null,
"aa_length": 1677,
"cds_start": 4919,
"cds_end": null,
"cds_length": 5034,
"cdna_start": 5314,
"cdna_end": null,
"cdna_length": 9237,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.4910_4913dupTTGA",
"hgvs_p": "p.Ser1639fs",
"transcript": "NM_001354420.2",
"protein_id": "NP_001341349.1",
"transcript_support_level": null,
"aa_start": 1638,
"aa_end": null,
"aa_length": 1675,
"cds_start": 4913,
"cds_end": null,
"cds_length": 5028,
"cdna_start": 5248,
"cdna_end": null,
"cdna_length": 9171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.3962_3965dupTTGA",
"hgvs_p": "p.Ser1323fs",
"transcript": "ENST00000642496.1",
"protein_id": "ENSP00000495930.1",
"transcript_support_level": null,
"aa_start": 1322,
"aa_end": null,
"aa_length": 1359,
"cds_start": 3965,
"cds_end": null,
"cds_length": 4080,
"cdna_start": 3967,
"cdna_end": null,
"cdna_length": 4335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.1265_1268dupTTGA",
"hgvs_p": "p.Ser424fs",
"transcript": "ENST00000618301.4",
"protein_id": "ENSP00000482780.1",
"transcript_support_level": 5,
"aa_start": 423,
"aa_end": null,
"aa_length": 460,
"cds_start": 1268,
"cds_end": null,
"cds_length": 1383,
"cdna_start": 1268,
"cdna_end": null,
"cdna_length": 1461,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.1133_1136dupTTGA",
"hgvs_p": "p.Ser380fs",
"transcript": "ENST00000495484.5",
"protein_id": "ENSP00000480780.1",
"transcript_support_level": 5,
"aa_start": 379,
"aa_end": null,
"aa_length": 416,
"cds_start": 1136,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 1527,
"cdna_end": null,
"cdna_length": 1896,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D*?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"hgvs_c": "c.4901_4904dupTTGA",
"hgvs_p": "p.Ser1636fs",
"transcript": "XM_047425663.1",
"protein_id": "XP_047281619.1",
"transcript_support_level": null,
"aa_start": 1635,
"aa_end": null,
"aa_length": 1672,
"cds_start": 4904,
"cds_end": null,
"cds_length": 5019,
"cdna_start": 5239,
"cdna_end": null,
"cdna_length": 9162,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PCDH15",
"gene_hgnc_id": 14674,
"dbsnp": "rs770322907",
"frequency_reference_population": 0.00006816514,
"hom_count_reference_population": 0,
"allele_count_reference_population": 110,
"gnomad_exomes_af": 0.0000677333,
"gnomad_genomes_af": 0.0000723142,
"gnomad_exomes_ac": 99,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 5.96,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PM2",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PVS1_Moderate",
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000644397.2",
"gene_symbol": "PCDH15",
"hgnc_id": 14674,
"effects": [
"frameshift_variant",
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.5105_5108dupTTGA",
"hgvs_p": "p.Ser1704fs"
}
],
"clinvar_disease": "Autosomal recessive nonsyndromic hearing loss 23,Usher syndrome type 1D,Usher syndrome type 1F,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "not specified|Autosomal recessive nonsyndromic hearing loss 23;Usher syndrome type 1D;Usher syndrome type 1F|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}