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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: 16-3408899-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=3408899&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"BP6"
],
"effects": [
"stop_gained"
],
"gene_symbol": "ZNF174",
"hgnc_id": 12963,
"hgvs_c": "c.1204C>T",
"hgvs_p": "p.Arg402*",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 1,
"transcript": "NM_003450.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 1,
"criteria": [
"PM2",
"PP3_Moderate",
"BP6"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000285329",
"hgnc_id": null,
"hgvs_c": "n.211+4251C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 4,
"score": 3,
"transcript": "ENST00000575785.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP6",
"acmg_score": 1,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.23,
"chr": "16",
"clinvar_classification": "Likely benign",
"clinvar_disease": "Long QT syndrome",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.23000000417232513,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 407,
"aa_ref": "R",
"aa_start": 402,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2459,
"cdna_start": 1994,
"cds_end": null,
"cds_length": 1224,
"cds_start": 1204,
"consequences": [
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_003450.3",
"gene_hgnc_id": 12963,
"gene_symbol": "ZNF174",
"hgvs_c": "c.1204C>T",
"hgvs_p": "p.Arg402*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000268655.5",
"protein_coding": true,
"protein_id": "NP_003441.1",
"strand": true,
"transcript": "NM_003450.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 407,
"aa_ref": "R",
"aa_start": 402,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2459,
"cdna_start": 1994,
"cds_end": null,
"cds_length": 1224,
"cds_start": 1204,
"consequences": [
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000268655.5",
"gene_hgnc_id": 12963,
"gene_symbol": "ZNF174",
"hgvs_c": "c.1204C>T",
"hgvs_p": "p.Arg402*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003450.3",
"protein_coding": true,
"protein_id": "ENSP00000268655.4",
"strand": true,
"transcript": "ENST00000268655.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 560,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000575785.2",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000285329",
"hgvs_c": "n.211+4251C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000477472.1",
"strand": true,
"transcript": "ENST00000575785.2",
"transcript_support_level": 4
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 407,
"aa_ref": "R",
"aa_start": 402,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1997,
"cdna_start": 1532,
"cds_end": null,
"cds_length": 1224,
"cds_start": 1204,
"consequences": [
"stop_gained"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001347868.2",
"gene_hgnc_id": 12963,
"gene_symbol": "ZNF174",
"hgvs_c": "c.1204C>T",
"hgvs_p": "p.Arg402*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001334797.1",
"strand": true,
"transcript": "NM_001347868.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 407,
"aa_ref": "R",
"aa_start": 402,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1586,
"cdna_start": 1512,
"cds_end": null,
"cds_length": 1224,
"cds_start": 1204,
"consequences": [
"stop_gained"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000571936.5",
"gene_hgnc_id": 12963,
"gene_symbol": "ZNF174",
"hgvs_c": "c.1204C>T",
"hgvs_p": "p.Arg402*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000460397.1",
"strand": true,
"transcript": "ENST00000571936.5",
"transcript_support_level": 5
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 401,
"aa_ref": "R",
"aa_start": 396,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2064,
"cdna_start": 1601,
"cds_end": null,
"cds_length": 1206,
"cds_start": 1186,
"consequences": [
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000959344.1",
"gene_hgnc_id": 12963,
"gene_symbol": "ZNF174",
"hgvs_c": "c.1186C>T",
"hgvs_p": "p.Arg396*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629403.1",
"strand": true,
"transcript": "ENST00000959344.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs761098156",
"effect": "stop_gained",
"frequency_reference_population": 0.000004802507,
"gene_hgnc_id": 12963,
"gene_symbol": "ZNF174",
"gnomad_exomes_ac": 7,
"gnomad_exomes_af": 0.00000480251,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "Long QT syndrome",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.028,
"pos": 3408899,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_003450.3"
}
]
}