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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: 8-96145185-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=96145185&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 96145185,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001001557.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDF6",
"gene_hgnc_id": 4221,
"hgvs_c": "c.746C>A",
"hgvs_p": "p.Ala249Glu",
"transcript": "NM_001001557.4",
"protein_id": "NP_001001557.1",
"transcript_support_level": null,
"aa_start": 249,
"aa_end": null,
"aa_length": 455,
"cds_start": 746,
"cds_end": null,
"cds_length": 1368,
"cdna_start": 860,
"cdna_end": null,
"cdna_length": 3712,
"mane_select": "ENST00000287020.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDF6",
"gene_hgnc_id": 4221,
"hgvs_c": "c.746C>A",
"hgvs_p": "p.Ala249Glu",
"transcript": "ENST00000287020.7",
"protein_id": "ENSP00000287020.4",
"transcript_support_level": 1,
"aa_start": 249,
"aa_end": null,
"aa_length": 455,
"cds_start": 746,
"cds_end": null,
"cds_length": 1368,
"cdna_start": 860,
"cdna_end": null,
"cdna_length": 3712,
"mane_select": "NM_001001557.4",
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GDF6",
"gene_hgnc_id": 4221,
"dbsnp": "rs121909352",
"frequency_reference_population": 0.0036674505,
"hom_count_reference_population": 16,
"allele_count_reference_population": 5489,
"gnomad_exomes_af": 0.00386103,
"gnomad_genomes_af": 0.00195769,
"gnomad_exomes_ac": 5191,
"gnomad_genomes_ac": 298,
"gnomad_exomes_homalt": 15,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03659674525260925,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.269,
"revel_prediction": "Benign",
"alphamissense_score": 0.0757,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.3,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.269,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001001557.4",
"gene_symbol": "GDF6",
"hgnc_id": 4221,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.746C>A",
"hgvs_p": "p.Ala249Glu"
}
],
"clinvar_disease": " autosomal dominant, isolated, with coloboma 6,Congenital anomaly of kidney and urinary tract,GDF6-related disorder,Isolated microphthalmia 4,Klippel-Feil syndrome,Klippel-Feil syndrome 1,Leber congenital amaurosis 17,Microphthalmia,Multiple synostoses syndrome 4,Retinal dystrophy,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:2 US:6 LB:3 B:1",
"phenotype_combined": "Klippel-Feil syndrome 1, autosomal dominant|Isolated microphthalmia 4|Leber congenital amaurosis 17|Klippel-Feil syndrome|not specified|not provided|Klippel-Feil syndrome 1, autosomal dominant;Congenital anomaly of kidney and urinary tract|Isolated microphthalmia 4;Leber congenital amaurosis 17;Klippel-Feil syndrome 1, autosomal dominant;Microphthalmia, isolated, with coloboma 6|Congenital anomaly of kidney and urinary tract|GDF6-related disorder|Isolated microphthalmia 4;Multiple synostoses syndrome 4;Leber congenital amaurosis 17;Klippel-Feil syndrome 1, autosomal dominant;Microphthalmia, isolated, with coloboma 6|Retinal dystrophy",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}