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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: 15-78515039-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=78515039&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 78515039,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001013619.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYKK",
"gene_hgnc_id": 34403,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Ile",
"transcript": "NM_001013619.4",
"protein_id": "NP_001013641.2",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 373,
"cds_start": 409,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 4197,
"mane_select": "ENST00000388988.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYKK",
"gene_hgnc_id": 34403,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Ile",
"transcript": "ENST00000388988.9",
"protein_id": "ENSP00000373640.4",
"transcript_support_level": 5,
"aa_start": 137,
"aa_end": null,
"aa_length": 373,
"cds_start": 409,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 4197,
"mane_select": "NM_001013619.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYKK",
"gene_hgnc_id": 34403,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Ile",
"transcript": "ENST00000566332.5",
"protein_id": "ENSP00000457154.1",
"transcript_support_level": 1,
"aa_start": 137,
"aa_end": null,
"aa_length": 226,
"cds_start": 409,
"cds_end": null,
"cds_length": 681,
"cdna_start": 469,
"cdna_end": null,
"cdna_length": 1422,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYKK",
"gene_hgnc_id": 34403,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Ile",
"transcript": "ENST00000569878.5",
"protein_id": "ENSP00000455459.1",
"transcript_support_level": 5,
"aa_start": 137,
"aa_end": null,
"aa_length": 373,
"cds_start": 409,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 409,
"cdna_end": null,
"cdna_length": 4097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYKK",
"gene_hgnc_id": 34403,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Ile",
"transcript": "NM_001083612.2",
"protein_id": "NP_001077081.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 220,
"cds_start": 409,
"cds_end": null,
"cds_length": 663,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYKK",
"gene_hgnc_id": 34403,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Ile",
"transcript": "ENST00000408962.6",
"protein_id": "ENSP00000386197.2",
"transcript_support_level": 5,
"aa_start": 137,
"aa_end": null,
"aa_length": 220,
"cds_start": 409,
"cds_end": null,
"cds_length": 663,
"cdna_start": 522,
"cdna_end": null,
"cdna_length": 847,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYKK",
"gene_hgnc_id": 34403,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Ile",
"transcript": "ENST00000563233.2",
"protein_id": "ENSP00000454850.1",
"transcript_support_level": 2,
"aa_start": 137,
"aa_end": null,
"aa_length": 220,
"cds_start": 409,
"cds_end": null,
"cds_length": 663,
"cdna_start": 409,
"cdna_end": null,
"cdna_length": 734,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYKK",
"gene_hgnc_id": 34403,
"hgvs_c": "n.409C>A",
"hgvs_p": null,
"transcript": "ENST00000566289.5",
"protein_id": "ENSP00000456614.1",
"transcript_support_level": 2,
"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": 2180,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HYKK",
"gene_hgnc_id": 34403,
"dbsnp": "rs762296061",
"frequency_reference_population": 0.0000020653106,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000206531,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.016207635402679443,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.048,
"revel_prediction": "Benign",
"alphamissense_score": 0.0623,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.8,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.016,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001013619.4",
"gene_symbol": "HYKK",
"hgnc_id": 34403,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Ile"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}