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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: 5-122077861-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=122077861&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 122077861,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000231004.5",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "c.125G>A",
"hgvs_p": "p.Trp42*",
"transcript": "NM_002317.7",
"protein_id": "NP_002308.2",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 417,
"cds_start": 125,
"cds_end": null,
"cds_length": 1254,
"cdna_start": 399,
"cdna_end": null,
"cdna_length": 5076,
"mane_select": "ENST00000231004.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "c.125G>A",
"hgvs_p": "p.Trp42*",
"transcript": "ENST00000231004.5",
"protein_id": "ENSP00000231004.4",
"transcript_support_level": 1,
"aa_start": 42,
"aa_end": null,
"aa_length": 417,
"cds_start": 125,
"cds_end": null,
"cds_length": 1254,
"cdna_start": 399,
"cdna_end": null,
"cdna_length": 5076,
"mane_select": "NM_002317.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "n.125G>A",
"hgvs_p": null,
"transcript": "ENST00000639739.2",
"protein_id": "ENSP00000492324.2",
"transcript_support_level": 5,
"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": 3771,
"mane_select": null,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRFBP1",
"gene_hgnc_id": 26333,
"hgvs_c": "c.*2536C>T",
"hgvs_p": null,
"transcript": "XM_017009111.3",
"protein_id": "XP_016864600.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 371,
"cds_start": -4,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"dbsnp": "rs886040966",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5899999737739563,
"computational_prediction_selected": "Pathogenic",
"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": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.957,
"phylop100way_prediction": "Uncertain_significance",
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000231004.5",
"gene_symbol": "LOX",
"hgnc_id": 6664,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD",
"hgvs_c": "c.125G>A",
"hgvs_p": "p.Trp42*"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "XM_017009111.3",
"gene_symbol": "SRFBP1",
"hgnc_id": 26333,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*2536C>T",
"hgvs_p": null
}
],
"clinvar_disease": " familial thoracic 10,Acute aortic dissection,Aortic aneurysm,Congenital aneurysm of ascending aorta,Familial thoracic aortic aneurysm and aortic dissection",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Aortic aneurysm, familial thoracic 10|Acute aortic dissection;Congenital aneurysm of ascending aorta|Familial thoracic aortic aneurysm and aortic dissection",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}