← Back to variant description
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: 19-50908495-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=50908495&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 50908495,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_004917.5",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"hgvs_c": "c.476G>A",
"hgvs_p": "p.Gly159Asp",
"transcript": "NM_004917.5",
"protein_id": "NP_004908.4",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 254,
"cds_start": 476,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000324041.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004917.5"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"hgvs_c": "c.476G>A",
"hgvs_p": "p.Gly159Asp",
"transcript": "ENST00000324041.6",
"protein_id": "ENSP00000326159.1",
"transcript_support_level": 1,
"aa_start": 159,
"aa_end": null,
"aa_length": 254,
"cds_start": 476,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004917.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000324041.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"hgvs_c": "c.328+84G>A",
"hgvs_p": null,
"transcript": "ENST00000431178.2",
"protein_id": "ENSP00000399448.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 110,
"cds_start": null,
"cds_end": null,
"cds_length": 333,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000431178.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"hgvs_c": "n.478G>A",
"hgvs_p": null,
"transcript": "ENST00000596876.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000596876.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"hgvs_c": "n.412G>A",
"hgvs_p": null,
"transcript": "ENST00000599865.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000599865.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"hgvs_c": "n.*260G>A",
"hgvs_p": null,
"transcript": "ENST00000602148.1",
"protein_id": "ENSP00000472091.1",
"transcript_support_level": 1,
"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": "nonsense_mediated_decay",
"feature": "ENST00000602148.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"hgvs_c": "n.*260G>A",
"hgvs_p": null,
"transcript": "ENST00000602148.1",
"protein_id": "ENSP00000472091.1",
"transcript_support_level": 1,
"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": "nonsense_mediated_decay",
"feature": "ENST00000602148.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"hgvs_c": "n.191-4G>A",
"hgvs_p": null,
"transcript": "ENST00000598305.5",
"protein_id": "ENSP00000469963.1",
"transcript_support_level": 1,
"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": "nonsense_mediated_decay",
"feature": "ENST00000598305.5"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"hgvs_c": "c.191G>A",
"hgvs_p": "p.Gly64Asp",
"transcript": "NM_001302961.2",
"protein_id": "NP_001289890.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 159,
"cds_start": 191,
"cds_end": null,
"cds_length": 480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001302961.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"hgvs_c": "c.476-4G>A",
"hgvs_p": null,
"transcript": "XM_011527545.4",
"protein_id": "XP_011525847.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 166,
"cds_start": null,
"cds_end": null,
"cds_length": 501,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011527545.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"hgvs_c": "n.191-4G>A",
"hgvs_p": null,
"transcript": "ENST00000593885.1",
"protein_id": "ENSP00000469769.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000593885.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"hgvs_c": "n.469-4G>A",
"hgvs_p": null,
"transcript": "NR_126566.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_126566.2"
}
],
"gene_symbol": "KLK4",
"gene_hgnc_id": 6365,
"dbsnp": "rs34626614",
"frequency_reference_population": 0.0032103106,
"hom_count_reference_population": 126,
"allele_count_reference_population": 5182,
"gnomad_exomes_af": 0.00186062,
"gnomad_genomes_af": 0.0161657,
"gnomad_exomes_ac": 2720,
"gnomad_genomes_ac": 2462,
"gnomad_exomes_homalt": 67,
"gnomad_genomes_homalt": 59,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.002964913845062256,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.34599998593330383,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.309,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2623,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.028,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0774694313635443,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -19,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 20,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_004917.5",
"gene_symbol": "KLK4",
"hgnc_id": 6365,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.476G>A",
"hgvs_p": "p.Gly159Asp"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}