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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: 1-196982883-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=196982883&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 196982883,
"ref": "A",
"alt": "C",
"effect": "splice_acceptor_variant,intron_variant",
"transcript": "NM_030787.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CFHR5",
"gene_hgnc_id": 24668,
"hgvs_c": "c.59-2A>C",
"hgvs_p": null,
"transcript": "NM_030787.4",
"protein_id": "NP_110414.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 569,
"cds_start": -4,
"cds_end": null,
"cds_length": 1710,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2814,
"mane_select": "ENST00000256785.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CFHR5",
"gene_hgnc_id": 24668,
"hgvs_c": "c.59-2A>C",
"hgvs_p": null,
"transcript": "ENST00000256785.5",
"protein_id": "ENSP00000256785.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 569,
"cds_start": -4,
"cds_end": null,
"cds_length": 1710,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2814,
"mane_select": "NM_030787.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CFHR5",
"gene_hgnc_id": 24668,
"hgvs_c": "c.-197-2A>C",
"hgvs_p": null,
"transcript": "ENST00000699466.1",
"protein_id": "ENSP00000514393.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 484,
"cds_start": -4,
"cds_end": null,
"cds_length": 1455,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2352,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CFHR5",
"gene_hgnc_id": 24668,
"hgvs_c": "c.-25+5203A>C",
"hgvs_p": null,
"transcript": "ENST00000699468.1",
"protein_id": "ENSP00000514394.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 267,
"cds_start": -4,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1545,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CFHR5",
"gene_hgnc_id": 24668,
"hgvs_c": "n.128-2A>C",
"hgvs_p": null,
"transcript": "ENST00000699467.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CFHR5",
"gene_hgnc_id": 24668,
"hgvs_c": "c.68-2A>C",
"hgvs_p": null,
"transcript": "XM_011510020.3",
"protein_id": "XP_011508322.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 572,
"cds_start": -4,
"cds_end": null,
"cds_length": 1719,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2728,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CFHR5",
"gene_hgnc_id": 24668,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8999999761581421,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.734000027179718,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.9,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.533,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.98,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999968624618023,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PVS1_Strong",
"PM2"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_030787.4",
"gene_symbol": "CFHR5",
"hgnc_id": 24668,
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.59-2A>C",
"hgvs_p": null
}
],
"clinvar_disease": "C3 glomerulonephritis",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "C3 glomerulonephritis",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}