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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: 1-215728232-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=215728232&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 215728232,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000307340.8",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 72,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.11864G>A",
"hgvs_p": "p.Trp3955*",
"transcript": "NM_206933.4",
"protein_id": "NP_996816.3",
"transcript_support_level": null,
"aa_start": 3955,
"aa_end": null,
"aa_length": 5202,
"cds_start": 11864,
"cds_end": null,
"cds_length": 15609,
"cdna_start": 12303,
"cdna_end": null,
"cdna_length": 18938,
"mane_select": "ENST00000307340.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 72,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.11864G>A",
"hgvs_p": "p.Trp3955*",
"transcript": "ENST00000307340.8",
"protein_id": "ENSP00000305941.3",
"transcript_support_level": 1,
"aa_start": 3955,
"aa_end": null,
"aa_length": 5202,
"cds_start": 11864,
"cds_end": null,
"cds_length": 15609,
"cdna_start": 12303,
"cdna_end": null,
"cdna_length": 18938,
"mane_select": "NM_206933.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 73,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.11864G>A",
"hgvs_p": "p.Trp3955*",
"transcript": "ENST00000674083.1",
"protein_id": "ENSP00000501296.1",
"transcript_support_level": null,
"aa_start": 3955,
"aa_end": null,
"aa_length": 5226,
"cds_start": 11864,
"cds_end": null,
"cds_length": 15681,
"cdna_start": 12303,
"cdna_end": null,
"cdna_length": 19010,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"dbsnp": "rs111033364",
"frequency_reference_population": 0.00010842842,
"hom_count_reference_population": 1,
"allele_count_reference_population": 175,
"gnomad_exomes_af": 0.000106712,
"gnomad_genomes_af": 0.000124926,
"gnomad_exomes_ac": 156,
"gnomad_genomes_ac": 19,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6600000262260437,
"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": 0.66,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.533,
"phylop100way_prediction": "Pathogenic",
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000307340.8",
"gene_symbol": "USH2A",
"hgnc_id": 12601,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.11864G>A",
"hgvs_p": "p.Trp3955*"
}
],
"clinvar_disease": "Congenital sensorineural hearing impairment,Hearing impairment,Rare genetic deafness,Retinal dystrophy,Retinitis pigmentosa,Retinitis pigmentosa 39,See cases,USH2A-related disorder,Usher syndrome,Usher syndrome type 2,Usher syndrome type 2A,Usher syndrome type 3A,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:28",
"phenotype_combined": "Usher syndrome type 2A|Retinitis pigmentosa 39|Congenital sensorineural hearing impairment|Hearing impairment|not provided|Retinitis pigmentosa|Rare genetic deafness;Usher syndrome|Usher syndrome type 2|Retinal dystrophy|USH2A-related disorder|Retinitis pigmentosa 39;Usher syndrome type 2A|Usher syndrome type 3A|Usher syndrome|See cases",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}