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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: 22-18169868-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=18169868&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 18169868,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000215794.8",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP18",
"gene_hgnc_id": 12616,
"hgvs_c": "c.652C>T",
"hgvs_p": "p.Gln218*",
"transcript": "NM_017414.4",
"protein_id": "NP_059110.2",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 372,
"cds_start": 652,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 811,
"cdna_end": null,
"cdna_length": 1858,
"mane_select": "ENST00000215794.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP18",
"gene_hgnc_id": 12616,
"hgvs_c": "c.652C>T",
"hgvs_p": "p.Gln218*",
"transcript": "ENST00000215794.8",
"protein_id": "ENSP00000215794.7",
"transcript_support_level": 1,
"aa_start": 218,
"aa_end": null,
"aa_length": 372,
"cds_start": 652,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 811,
"cdna_end": null,
"cdna_length": 1858,
"mane_select": "NM_017414.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP18",
"gene_hgnc_id": 12616,
"hgvs_c": "c.652C>T",
"hgvs_p": "p.Gln218*",
"transcript": "ENST00000699060.2",
"protein_id": "ENSP00000514107.1",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 316,
"cds_start": 652,
"cds_end": null,
"cds_length": 951,
"cdna_start": 1138,
"cdna_end": null,
"cdna_length": 1988,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP18",
"gene_hgnc_id": 12616,
"hgvs_c": "c.430C>T",
"hgvs_p": "p.Gln144*",
"transcript": "XM_006724074.4",
"protein_id": "XP_006724137.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 298,
"cds_start": 430,
"cds_end": null,
"cds_length": 897,
"cdna_start": 582,
"cdna_end": null,
"cdna_length": 1629,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP18",
"gene_hgnc_id": 12616,
"hgvs_c": "n.398C>T",
"hgvs_p": null,
"transcript": "ENST00000699061.1",
"protein_id": null,
"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": 685,
"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": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP18",
"gene_hgnc_id": 12616,
"hgvs_c": "n.*526C>T",
"hgvs_p": null,
"transcript": "ENST00000715585.1",
"protein_id": "ENSP00000520484.1",
"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": 1897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP18",
"gene_hgnc_id": 12616,
"hgvs_c": "n.*526C>T",
"hgvs_p": null,
"transcript": "ENST00000715585.1",
"protein_id": "ENSP00000520484.1",
"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": 1897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "USP18",
"gene_hgnc_id": 12616,
"dbsnp": "rs1085307118",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6000000238418579,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.882,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.1,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000215794.8",
"gene_symbol": "USP18",
"hgnc_id": 12616,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.652C>T",
"hgvs_p": "p.Gln218*"
}
],
"clinvar_disease": "Pseudo-TORCH syndrome 2",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Pseudo-TORCH syndrome 2",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}