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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: 1-169529762-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=169529762&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 169529762,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000367797.9",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F5",
"gene_hgnc_id": 3542,
"hgvs_c": "c.5265A>G",
"hgvs_p": "p.Ile1755Met",
"transcript": "NM_000130.5",
"protein_id": "NP_000121.2",
"transcript_support_level": null,
"aa_start": 1755,
"aa_end": null,
"aa_length": 2224,
"cds_start": 5265,
"cds_end": null,
"cds_length": 6675,
"cdna_start": 5360,
"cdna_end": null,
"cdna_length": 9132,
"mane_select": "ENST00000367797.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F5",
"gene_hgnc_id": 3542,
"hgvs_c": "c.5265A>G",
"hgvs_p": "p.Ile1755Met",
"transcript": "ENST00000367797.9",
"protein_id": "ENSP00000356771.3",
"transcript_support_level": 1,
"aa_start": 1755,
"aa_end": null,
"aa_length": 2224,
"cds_start": 5265,
"cds_end": null,
"cds_length": 6675,
"cdna_start": 5360,
"cdna_end": null,
"cdna_length": 9132,
"mane_select": "NM_000130.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F5",
"gene_hgnc_id": 3542,
"hgvs_c": "c.5280A>G",
"hgvs_p": "p.Ile1760Met",
"transcript": "ENST00000367796.3",
"protein_id": "ENSP00000356770.3",
"transcript_support_level": 5,
"aa_start": 1760,
"aa_end": null,
"aa_length": 2229,
"cds_start": 5280,
"cds_end": null,
"cds_length": 6690,
"cdna_start": 5482,
"cdna_end": null,
"cdna_length": 7039,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "F5",
"gene_hgnc_id": 3542,
"dbsnp": "rs41272455",
"frequency_reference_population": 0.0010651957,
"hom_count_reference_population": 1,
"allele_count_reference_population": 1719,
"gnomad_exomes_af": 0.00106468,
"gnomad_genomes_af": 0.00107017,
"gnomad_exomes_ac": 1556,
"gnomad_genomes_ac": 163,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.011879801750183105,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.3,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0894,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.538,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BS1_Supporting",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000367797.9",
"gene_symbol": "F5",
"hgnc_id": 3542,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.5265A>G",
"hgvs_p": "p.Ile1755Met"
}
],
"clinvar_disease": " 1, recurrent, susceptibility to,Budd-Chiari syndrome,Congenital factor V deficiency,F5-related disorder,Factor V deficiency,Hemorrhage,Inborn genetic diseases,Ischemic stroke,Pregnancy loss,Thrombophilia due to activated protein C resistance,Thrombophilia due to thrombin defect,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:9 LB:1",
"phenotype_combined": "Factor V deficiency|Thrombophilia due to activated protein C resistance;Factor V deficiency;Ischemic stroke;Budd-Chiari syndrome;Pregnancy loss, recurrent, susceptibility to, 1|Thrombophilia due to activated protein C resistance|not provided|Inborn genetic diseases|Budd-Chiari syndrome|Congenital factor V deficiency|Hemorrhage|Thrombophilia due to thrombin defect|F5-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}