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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: 11-46739505-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=46739505&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 46739505,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant",
"transcript": "ENST00000311907.10",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F2",
"gene_hgnc_id": 3535,
"hgvs_c": "c.*97G>A",
"hgvs_p": null,
"transcript": "NM_000506.5",
"protein_id": "NP_000497.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 622,
"cds_start": -4,
"cds_end": null,
"cds_length": 1869,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1990,
"mane_select": "ENST00000311907.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F2",
"gene_hgnc_id": 3535,
"hgvs_c": "c.*97G>A",
"hgvs_p": null,
"transcript": "ENST00000311907.10",
"protein_id": "ENSP00000308541.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 622,
"cds_start": -4,
"cds_end": null,
"cds_length": 1869,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1990,
"mane_select": "NM_000506.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F2",
"gene_hgnc_id": 3535,
"hgvs_c": "c.*97G>A",
"hgvs_p": null,
"transcript": "NM_000506.5",
"protein_id": "NP_000497.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 622,
"cds_start": -4,
"cds_end": null,
"cds_length": 1869,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1990,
"mane_select": "ENST00000311907.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F2",
"gene_hgnc_id": 3535,
"hgvs_c": "c.*97G>A",
"hgvs_p": null,
"transcript": "ENST00000311907.10",
"protein_id": "ENSP00000308541.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 622,
"cds_start": -4,
"cds_end": null,
"cds_length": 1869,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1990,
"mane_select": "NM_000506.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F2",
"gene_hgnc_id": 3535,
"hgvs_c": "c.*97G>A",
"hgvs_p": null,
"transcript": "ENST00000530231.5",
"protein_id": "ENSP00000433907.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 583,
"cds_start": -4,
"cds_end": null,
"cds_length": 1752,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1849,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "F2",
"gene_hgnc_id": 3535,
"dbsnp": "rs1799963",
"frequency_reference_population": 0.011384997,
"hom_count_reference_population": 136,
"allele_count_reference_population": 16850,
"gnomad_exomes_af": 0.0115936,
"gnomad_genomes_af": 0.00956639,
"gnomad_exomes_ac": 15393,
"gnomad_genomes_ac": 1457,
"gnomad_exomes_homalt": 118,
"gnomad_genomes_homalt": 18,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7099999785423279,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.71,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.878,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP5_Very_Strong,BP4,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 6,
"pathogenic_score": 8,
"criteria": [
"PP5_Very_Strong",
"BP4",
"BS1_Supporting",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000311907.10",
"gene_symbol": "F2",
"hgnc_id": 3535,
"effects": [
"splice_region_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.*97G>A",
"hgvs_p": null
}
],
"clinvar_disease": " 2, recurrent, susceptibility to,Cerebral palsy,Congenital prothrombin deficiency,Ischemic stroke,Pregnancy loss,Thrombophilia caused by F2 prothrombin deficiency,Thrombophilia due to thrombin defect,Venous thromboembolism,not provided",
"clinvar_classification": " low penetrance, risk factor,Pathogenic/Likely pathogenic/Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:15 LP:1 US:1 O:3",
"phenotype_combined": "Ischemic stroke|Pregnancy loss, recurrent, susceptibility to, 2|Congenital prothrombin deficiency|Venous thromboembolism|not provided|Cerebral palsy|Thrombophilia caused by F2 prothrombin deficiency|Congenital prothrombin deficiency;Pregnancy loss, recurrent, susceptibility to, 2;Ischemic stroke;Thrombophilia due to thrombin defect|Thrombophilia due to thrombin defect",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic/Pathogenic, low penetrance; risk factor",
"custom_annotations": null
}
],
"message": null
}