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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: 4-122742955-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=122742955&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 122742955,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000314218.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS12",
"gene_hgnc_id": 26648,
"hgvs_c": "c.1063C>T",
"hgvs_p": "p.Arg355*",
"transcript": "NM_152618.3",
"protein_id": "NP_689831.2",
"transcript_support_level": null,
"aa_start": 355,
"aa_end": null,
"aa_length": 710,
"cds_start": 1063,
"cds_end": null,
"cds_length": 2133,
"cdna_start": 1254,
"cdna_end": null,
"cdna_length": 3238,
"mane_select": "ENST00000314218.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS12",
"gene_hgnc_id": 26648,
"hgvs_c": "c.1063C>T",
"hgvs_p": "p.Arg355*",
"transcript": "ENST00000314218.8",
"protein_id": "ENSP00000319062.3",
"transcript_support_level": 1,
"aa_start": 355,
"aa_end": null,
"aa_length": 710,
"cds_start": 1063,
"cds_end": null,
"cds_length": 2133,
"cdna_start": 1254,
"cdna_end": null,
"cdna_length": 3238,
"mane_select": "NM_152618.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS12",
"gene_hgnc_id": 26648,
"hgvs_c": "c.1063C>T",
"hgvs_p": "p.Arg355*",
"transcript": "NM_001178007.2",
"protein_id": "NP_001171478.1",
"transcript_support_level": null,
"aa_start": 355,
"aa_end": null,
"aa_length": 710,
"cds_start": 1063,
"cds_end": null,
"cds_length": 2133,
"cdna_start": 1442,
"cdna_end": null,
"cdna_length": 3426,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS12",
"gene_hgnc_id": 26648,
"hgvs_c": "c.1063C>T",
"hgvs_p": "p.Arg355*",
"transcript": "ENST00000542236.5",
"protein_id": "ENSP00000438273.1",
"transcript_support_level": 2,
"aa_start": 355,
"aa_end": null,
"aa_length": 710,
"cds_start": 1063,
"cds_end": null,
"cds_length": 2133,
"cdna_start": 1444,
"cdna_end": null,
"cdna_length": 3431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS12",
"gene_hgnc_id": 26648,
"hgvs_c": "c.1063C>T",
"hgvs_p": "p.Arg355*",
"transcript": "XM_011531680.3",
"protein_id": "XP_011529982.1",
"transcript_support_level": null,
"aa_start": 355,
"aa_end": null,
"aa_length": 710,
"cds_start": 1063,
"cds_end": null,
"cds_length": 2133,
"cdna_start": 1198,
"cdna_end": null,
"cdna_length": 3182,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BBS12",
"gene_hgnc_id": 26648,
"dbsnp": "rs121918327",
"frequency_reference_population": 0.000017347731,
"hom_count_reference_population": 0,
"allele_count_reference_population": 28,
"gnomad_exomes_af": 0.0000177859,
"gnomad_genomes_af": 0.0000131396,
"gnomad_exomes_ac": 26,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.28999999165534973,
"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": 0.29,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.189,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000314218.8",
"gene_symbol": "BBS12",
"hgnc_id": 26648,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1063C>T",
"hgvs_p": "p.Arg355*"
}
],
"clinvar_disease": " postaxial, type A1,Abnormal cardiovascular system morphology,Bardet-Biedl syndrome,Bardet-Biedl syndrome 1,Bardet-Biedl syndrome 12,Inability to walk,Polydactyly,Visual impairment,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:10",
"phenotype_combined": "Bardet-Biedl syndrome 12|Bardet-Biedl syndrome|Inability to walk;Visual impairment;Abnormal cardiovascular system morphology;Polydactyly, postaxial, type A1|Bardet-Biedl syndrome 1|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}