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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: 18-199231-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=199231&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 199231,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000261601.8",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.791A>T",
"hgvs_p": "p.Glu264Val",
"transcript": "NM_005151.4",
"protein_id": "NP_005142.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 494,
"cds_start": 791,
"cds_end": null,
"cds_length": 1485,
"cdna_start": 933,
"cdna_end": null,
"cdna_length": 4972,
"mane_select": "ENST00000261601.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.791A>T",
"hgvs_p": "p.Glu264Val",
"transcript": "ENST00000261601.8",
"protein_id": "ENSP00000261601.6",
"transcript_support_level": 1,
"aa_start": 264,
"aa_end": null,
"aa_length": 494,
"cds_start": 791,
"cds_end": null,
"cds_length": 1485,
"cdna_start": 933,
"cdna_end": null,
"cdna_length": 4972,
"mane_select": "NM_005151.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.758A>T",
"hgvs_p": "p.Glu253Val",
"transcript": "ENST00000400266.7",
"protein_id": "ENSP00000383125.3",
"transcript_support_level": 2,
"aa_start": 253,
"aa_end": null,
"aa_length": 483,
"cds_start": 758,
"cds_end": null,
"cds_length": 1452,
"cdna_start": 921,
"cdna_end": null,
"cdna_length": 1681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.686A>T",
"hgvs_p": "p.Glu229Val",
"transcript": "NM_001037334.2",
"protein_id": "NP_001032411.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 459,
"cds_start": 686,
"cds_end": null,
"cds_length": 1380,
"cdna_start": 828,
"cdna_end": null,
"cdna_length": 4867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.686A>T",
"hgvs_p": "p.Glu229Val",
"transcript": "ENST00000582707.5",
"protein_id": "ENSP00000464447.1",
"transcript_support_level": 5,
"aa_start": 229,
"aa_end": null,
"aa_length": 459,
"cds_start": 686,
"cds_end": null,
"cds_length": 1380,
"cdna_start": 1002,
"cdna_end": null,
"cdna_length": 1803,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.653A>T",
"hgvs_p": "p.Glu218Val",
"transcript": "ENST00000383589.6",
"protein_id": "ENSP00000373083.2",
"transcript_support_level": 5,
"aa_start": 218,
"aa_end": null,
"aa_length": 448,
"cds_start": 653,
"cds_end": null,
"cds_length": 1347,
"cdna_start": 761,
"cdna_end": null,
"cdna_length": 2168,
"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": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "n.426A>T",
"hgvs_p": null,
"transcript": "ENST00000578786.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 1104,
"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": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "n.824A>T",
"hgvs_p": null,
"transcript": "ENST00000578942.5",
"protein_id": null,
"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": 3189,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"dbsnp": "rs776814532",
"frequency_reference_population": 0.000050813574,
"hom_count_reference_population": 0,
"allele_count_reference_population": 82,
"gnomad_exomes_af": 0.0000492639,
"gnomad_genomes_af": 0.0000656918,
"gnomad_exomes_ac": 72,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.45667463541030884,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.24,
"revel_prediction": "Benign",
"alphamissense_score": 0.1063,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.706,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000261601.8",
"gene_symbol": "USP14",
"hgnc_id": 12612,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.791A>T",
"hgvs_p": "p.Glu264Val"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}