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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: 20-44186480-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=44186480&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 44186480,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000372980.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JPH2",
"gene_hgnc_id": 14202,
"hgvs_c": "c.226A>T",
"hgvs_p": "p.Thr76Ser",
"transcript": "NM_020433.5",
"protein_id": "NP_065166.2",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 696,
"cds_start": 226,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 9502,
"mane_select": "ENST00000372980.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JPH2",
"gene_hgnc_id": 14202,
"hgvs_c": "c.226A>T",
"hgvs_p": "p.Thr76Ser",
"transcript": "ENST00000372980.4",
"protein_id": "ENSP00000362071.3",
"transcript_support_level": 5,
"aa_start": 76,
"aa_end": null,
"aa_length": 696,
"cds_start": 226,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 9502,
"mane_select": "NM_020433.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JPH2",
"gene_hgnc_id": 14202,
"hgvs_c": "c.226A>T",
"hgvs_p": "p.Thr76Ser",
"transcript": "ENST00000342272.3",
"protein_id": "ENSP00000344590.3",
"transcript_support_level": 1,
"aa_start": 76,
"aa_end": null,
"aa_length": 129,
"cds_start": 226,
"cds_end": null,
"cds_length": 390,
"cdna_start": 614,
"cdna_end": null,
"cdna_length": 1923,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JPH2",
"gene_hgnc_id": 14202,
"hgvs_c": "c.226A>T",
"hgvs_p": "p.Thr76Ser",
"transcript": "NM_175913.4",
"protein_id": "NP_787109.2",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 129,
"cds_start": 226,
"cds_end": null,
"cds_length": 390,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 2018,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JPH2",
"gene_hgnc_id": 14202,
"hgvs_c": "c.226A>T",
"hgvs_p": "p.Thr76Ser",
"transcript": "XM_006723833.5",
"protein_id": "XP_006723896.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 147,
"cds_start": 226,
"cds_end": null,
"cds_length": 444,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 11676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "JPH2",
"gene_hgnc_id": 14202,
"dbsnp": "rs764474492",
"frequency_reference_population": 6.8405535e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84055e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.23776820302009583,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.13,
"revel_prediction": "Benign",
"alphamissense_score": 0.1039,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.933,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000372980.4",
"gene_symbol": "JPH2",
"hgnc_id": 14202,
"effects": [
"missense_variant"
],
"inheritance_mode": "SD,AD,Unknown,AR",
"hgvs_c": "c.226A>T",
"hgvs_p": "p.Thr76Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}