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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: 5-144473992-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=144473992&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "KCTD16",
"hgnc_id": 29244,
"hgvs_c": "c.1165C>T",
"hgvs_p": "p.Leu389Phe",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_020768.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 335,
"alphamissense_prediction": null,
"alphamissense_score": 0.1711,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.4,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.005680263042449951,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 428,
"aa_ref": "L",
"aa_start": 389,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13488,
"cdna_start": 1794,
"cds_end": null,
"cds_length": 1287,
"cds_start": 1165,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_020768.4",
"gene_hgnc_id": 29244,
"gene_symbol": "KCTD16",
"hgvs_c": "c.1165C>T",
"hgvs_p": "p.Leu389Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000512467.6",
"protein_coding": true,
"protein_id": "NP_065819.1",
"strand": true,
"transcript": "NM_020768.4",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 428,
"aa_ref": "L",
"aa_start": 389,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 13488,
"cdna_start": 1794,
"cds_end": null,
"cds_length": 1287,
"cds_start": 1165,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000512467.6",
"gene_hgnc_id": 29244,
"gene_symbol": "KCTD16",
"hgvs_c": "c.1165C>T",
"hgvs_p": "p.Leu389Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_020768.4",
"protein_coding": true,
"protein_id": "ENSP00000424151.1",
"strand": true,
"transcript": "ENST00000512467.6",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 428,
"aa_ref": "L",
"aa_start": 389,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13950,
"cdna_start": 2256,
"cds_end": null,
"cds_length": 1287,
"cds_start": 1165,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000507359.3",
"gene_hgnc_id": 29244,
"gene_symbol": "KCTD16",
"hgvs_c": "c.1165C>T",
"hgvs_p": "p.Leu389Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000426548.1",
"strand": true,
"transcript": "ENST00000507359.3",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 428,
"aa_ref": "L",
"aa_start": 389,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13836,
"cdna_start": 2142,
"cds_end": null,
"cds_length": 1287,
"cds_start": 1165,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001370486.1",
"gene_hgnc_id": 29244,
"gene_symbol": "KCTD16",
"hgvs_c": "c.1165C>T",
"hgvs_p": "p.Leu389Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001357415.1",
"strand": true,
"transcript": "NM_001370486.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 428,
"aa_ref": "L",
"aa_start": 389,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13896,
"cdna_start": 2202,
"cds_end": null,
"cds_length": 1287,
"cds_start": 1165,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001370487.1",
"gene_hgnc_id": 29244,
"gene_symbol": "KCTD16",
"hgvs_c": "c.1165C>T",
"hgvs_p": "p.Leu389Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001357416.1",
"strand": true,
"transcript": "NM_001370487.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 428,
"aa_ref": "L",
"aa_start": 389,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13344,
"cdna_start": 1650,
"cds_end": null,
"cds_length": 1287,
"cds_start": 1165,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_005268493.3",
"gene_hgnc_id": 29244,
"gene_symbol": "KCTD16",
"hgvs_c": "c.1165C>T",
"hgvs_p": "p.Leu389Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005268550.1",
"strand": true,
"transcript": "XM_005268493.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs141010798",
"effect": "missense_variant",
"frequency_reference_population": 0.00020756786,
"gene_hgnc_id": 29244,
"gene_symbol": "KCTD16",
"gnomad_exomes_ac": 267,
"gnomad_exomes_af": 0.000182647,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 68,
"gnomad_genomes_af": 0.000447092,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.019,
"pos": 144473992,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.12,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_020768.4"
}
]
}