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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: 10-71793532-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=71793532&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 71793532,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000224721.12",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.6604G>A",
"hgvs_p": "p.Asp2202Asn",
"transcript": "NM_022124.6",
"protein_id": "NP_071407.4",
"transcript_support_level": null,
"aa_start": 2202,
"aa_end": null,
"aa_length": 3354,
"cds_start": 6604,
"cds_end": null,
"cds_length": 10065,
"cdna_start": 7008,
"cdna_end": null,
"cdna_length": 11138,
"mane_select": "ENST00000224721.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.6604G>A",
"hgvs_p": "p.Asp2202Asn",
"transcript": "ENST00000224721.12",
"protein_id": "ENSP00000224721.9",
"transcript_support_level": 5,
"aa_start": 2202,
"aa_end": null,
"aa_length": 3354,
"cds_start": 6604,
"cds_end": null,
"cds_length": 10065,
"cdna_start": 7008,
"cdna_end": null,
"cdna_length": 11138,
"mane_select": "NM_022124.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "n.-105G>A",
"hgvs_p": null,
"transcript": "ENST00000642965.1",
"protein_id": "ENSP00000495222.1",
"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": 4380,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"dbsnp": "rs121908349",
"frequency_reference_population": 0.0000030987228,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000273693,
"gnomad_genomes_af": 0.00000657557,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9740972518920898,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.732,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9025,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.002,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000224721.12",
"gene_symbol": "CDH23",
"hgnc_id": 13733,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.6604G>A",
"hgvs_p": "p.Asp2202Asn"
}
],
"clinvar_disease": " autosomal recessive, multiple types,Autosomal recessive nonsyndromic hearing loss 12,Hearing loss,Pituitary adenoma 5,Usher syndrome,Usher syndrome type 1,Usher syndrome type 1D,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:3",
"phenotype_combined": "Autosomal recessive nonsyndromic hearing loss 12|not provided|Pituitary adenoma 5, multiple types|Hearing loss, autosomal recessive|Pituitary adenoma 5, multiple types;Usher syndrome type 1D;Autosomal recessive nonsyndromic hearing loss 12|Usher syndrome type 1|Usher syndrome",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}