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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: 19-50827671-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=50827671&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "KLK15",
"hgnc_id": 20453,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Cys63Tyr",
"inheritance_mode": "AR",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_017509.4",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_score": 6,
"allele_count_reference_population": 12,
"alphamissense_prediction": null,
"alphamissense_score": 0.989,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.46,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9700057506561279,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 256,
"aa_ref": "C",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1357,
"cdna_start": 267,
"cds_end": null,
"cds_length": 771,
"cds_start": 188,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_017509.4",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Cys63Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000598239.6",
"protein_coding": true,
"protein_id": "NP_059979.2",
"strand": false,
"transcript": "NM_017509.4",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 256,
"aa_ref": "C",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1357,
"cdna_start": 267,
"cds_end": null,
"cds_length": 771,
"cds_start": 188,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000598239.6",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Cys63Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_017509.4",
"protein_coding": true,
"protein_id": "ENSP00000469315.1",
"strand": false,
"transcript": "ENST00000598239.6",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 160,
"aa_ref": "C",
"aa_start": 62,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 692,
"cdna_start": 206,
"cds_end": null,
"cds_length": 483,
"cds_start": 185,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000596931.5",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.185G>A",
"hgvs_p": "p.Cys62Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000471164.1",
"strand": false,
"transcript": "ENST00000596931.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1398,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000601680.1",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "n.188G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000601680.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 711,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000602114.1",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "n.185G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468856.1",
"strand": false,
"transcript": "ENST00000602114.1",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 256,
"aa_ref": "C",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1831,
"cdna_start": 757,
"cds_end": null,
"cds_length": 771,
"cds_start": 188,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000906215.1",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Cys63Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576274.1",
"strand": false,
"transcript": "ENST00000906215.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 256,
"aa_ref": "C",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1413,
"cdna_start": 346,
"cds_end": null,
"cds_length": 771,
"cds_start": 188,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000952480.1",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Cys63Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622539.1",
"strand": false,
"transcript": "ENST00000952480.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 255,
"aa_ref": "C",
"aa_start": 62,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1354,
"cdna_start": 264,
"cds_end": null,
"cds_length": 768,
"cds_start": 185,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001277081.2",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.185G>A",
"hgvs_p": "p.Cys62Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001264010.1",
"strand": false,
"transcript": "NM_001277081.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 255,
"aa_ref": "C",
"aa_start": 62,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1389,
"cdna_start": 315,
"cds_end": null,
"cds_length": 768,
"cds_start": 185,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000326856.8",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.185G>A",
"hgvs_p": "p.Cys62Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000314783.4",
"strand": false,
"transcript": "ENST00000326856.8",
"transcript_support_level": 5
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 255,
"aa_ref": "C",
"aa_start": 62,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1417,
"cdna_start": 328,
"cds_end": null,
"cds_length": 768,
"cds_start": 185,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000695998.1",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.185G>A",
"hgvs_p": "p.Cys62Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512319.1",
"strand": false,
"transcript": "ENST00000695998.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 255,
"aa_ref": "C",
"aa_start": 62,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1385,
"cdna_start": 311,
"cds_end": null,
"cds_length": 768,
"cds_start": 185,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000906216.1",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.185G>A",
"hgvs_p": "p.Cys62Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576275.1",
"strand": false,
"transcript": "ENST00000906216.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 171,
"aa_ref": "C",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1859,
"cdna_start": 1024,
"cds_end": null,
"cds_length": 516,
"cds_start": 188,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000695965.1",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Cys63Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512291.1",
"strand": false,
"transcript": "ENST00000695965.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 160,
"aa_ref": "C",
"aa_start": 62,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1217,
"cdna_start": 264,
"cds_end": null,
"cds_length": 483,
"cds_start": 185,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001277082.2",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.185G>A",
"hgvs_p": "p.Cys62Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001264011.1",
"strand": false,
"transcript": "NM_001277082.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 171,
"aa_ref": "C",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1102,
"cdna_start": 267,
"cds_end": null,
"cds_length": 516,
"cds_start": 188,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_011527087.3",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Cys63Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011525389.1",
"strand": false,
"transcript": "XM_011527087.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 170,
"aa_ref": "C",
"aa_start": 62,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1099,
"cdna_start": 264,
"cds_end": null,
"cds_length": 513,
"cds_start": 185,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047439064.1",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.185G>A",
"hgvs_p": "p.Cys62Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295020.1",
"strand": false,
"transcript": "XM_047439064.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 161,
"aa_ref": "C",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1220,
"cdna_start": 267,
"cds_end": null,
"cds_length": 486,
"cds_start": 188,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_011527088.3",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Cys63Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011525390.1",
"strand": false,
"transcript": "XM_011527088.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 121,
"aa_ref": "C",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 531,
"cdna_start": 267,
"cds_end": null,
"cds_length": 366,
"cds_start": 188,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_017026943.2",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Cys63Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882432.1",
"strand": false,
"transcript": "XM_017026943.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 42,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 374,
"cdna_start": null,
"cds_end": null,
"cds_length": 130,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000598673.1",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "c.-14G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000472523.1",
"strand": false,
"transcript": "ENST00000598673.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1188,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NR_102274.1",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "n.216G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_102274.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1006,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000695963.1",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "n.44-510G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000695963.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 869,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000695964.1",
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"hgvs_c": "n.44-510G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000695964.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs370799428",
"effect": "missense_variant",
"frequency_reference_population": 0.000007450427,
"gene_hgnc_id": 20453,
"gene_symbol": "KLK15",
"gnomad_exomes_ac": 7,
"gnomad_exomes_af": 0.00000479762,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000329841,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.811,
"pos": 50827671,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.911,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_017509.4"
}
]
}