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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: 19-50025640-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=50025640&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 50025640,
"ref": "C",
"alt": "T",
"effect": "5_prime_UTR_variant",
"transcript": "ENST00000599538.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK3",
"gene_hgnc_id": 18996,
"hgvs_c": "c.-359G>A",
"hgvs_p": null,
"transcript": "ENST00000599538.5",
"protein_id": "ENSP00000469880.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 474,
"cds_start": -4,
"cds_end": null,
"cds_length": 1425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2126,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "VRK3",
"gene_hgnc_id": 18996,
"hgvs_c": "c.-65+28G>A",
"hgvs_p": null,
"transcript": "ENST00000596445.5",
"protein_id": "ENSP00000469092.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": -4,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.-552C>T",
"hgvs_p": null,
"transcript": "ENST00000391821.6",
"protein_id": "ENSP00000375697.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 871,
"cds_start": -4,
"cds_end": null,
"cds_length": 2616,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.-577C>T",
"hgvs_p": null,
"transcript": "ENST00000595661.5",
"protein_id": "ENSP00000472808.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 871,
"cds_start": -4,
"cds_end": null,
"cds_length": 2616,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK3",
"gene_hgnc_id": 18996,
"hgvs_c": "c.-359G>A",
"hgvs_p": null,
"transcript": "ENST00000601341.5",
"protein_id": "ENSP00000470156.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 424,
"cds_start": -4,
"cds_end": null,
"cds_length": 1275,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1777,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK3",
"gene_hgnc_id": 18996,
"hgvs_c": "c.-359G>A",
"hgvs_p": null,
"transcript": "ENST00000600259.5",
"protein_id": "ENSP00000469400.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 149,
"cds_start": -4,
"cds_end": null,
"cds_length": 451,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.-455C>T",
"hgvs_p": null,
"transcript": "ENST00000598809.5",
"protein_id": "ENSP00000470956.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 73,
"cds_start": -4,
"cds_end": null,
"cds_length": 224,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 605,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK3",
"gene_hgnc_id": 18996,
"hgvs_c": "n.-201G>A",
"hgvs_p": null,
"transcript": "ENST00000599138.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 503,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VRK3",
"gene_hgnc_id": 18996,
"dbsnp": "rs245111",
"frequency_reference_population": 0.5305902,
"hom_count_reference_population": 23488,
"allele_count_reference_population": 80568,
"gnomad_exomes_af": 0.428571,
"gnomad_genomes_af": 0.530609,
"gnomad_exomes_ac": 12,
"gnomad_genomes_ac": 80556,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 23486,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7799999713897705,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"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": -0.78,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.528,
"phylop100way_prediction": "Benign",
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000599538.5",
"gene_symbol": "VRK3",
"hgnc_id": 18996,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-359G>A",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000391821.6",
"gene_symbol": "ZNF473",
"hgnc_id": 23239,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-552C>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}