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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: 18-163305-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=163305&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 163305,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "NM_005151.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.17-3C>T",
"hgvs_p": null,
"transcript": "NM_005151.4",
"protein_id": "NP_005142.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 494,
"cds_start": -4,
"cds_end": null,
"cds_length": 1485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4972,
"mane_select": "ENST00000261601.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.17-3C>T",
"hgvs_p": null,
"transcript": "ENST00000261601.8",
"protein_id": "ENSP00000261601.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 494,
"cds_start": -4,
"cds_end": null,
"cds_length": 1485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4972,
"mane_select": "NM_005151.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.17-3C>T",
"hgvs_p": null,
"transcript": "ENST00000400266.7",
"protein_id": "ENSP00000383125.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 483,
"cds_start": -4,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.17-3C>T",
"hgvs_p": null,
"transcript": "NM_001037334.2",
"protein_id": "NP_001032411.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 459,
"cds_start": -4,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.17-3C>T",
"hgvs_p": null,
"transcript": "ENST00000582707.5",
"protein_id": "ENSP00000464447.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 459,
"cds_start": -4,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1803,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.17-3C>T",
"hgvs_p": null,
"transcript": "ENST00000383589.6",
"protein_id": "ENSP00000373083.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 448,
"cds_start": -4,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"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": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.-62-3C>T",
"hgvs_p": null,
"transcript": "ENST00000581983.1",
"protein_id": "ENSP00000462315.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 27,
"cds_start": -4,
"cds_end": null,
"cds_length": 85,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 503,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "c.-62-3C>T",
"hgvs_p": null,
"transcript": "ENST00000580410.5",
"protein_id": "ENSP00000463891.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 19,
"cds_start": -4,
"cds_end": null,
"cds_length": 62,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 474,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "n.155-3C>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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"hgvs_c": "n.-89C>T",
"hgvs_p": null,
"transcript": "ENST00000583119.5",
"protein_id": "ENSP00000473563.1",
"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": 578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "USP14",
"gene_hgnc_id": 12612,
"dbsnp": "rs368077279",
"frequency_reference_population": 0.0002442477,
"hom_count_reference_population": 0,
"allele_count_reference_population": 391,
"gnomad_exomes_af": 0.000143581,
"gnomad_genomes_af": 0.00120254,
"gnomad_exomes_ac": 208,
"gnomad_genomes_ac": 183,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.18000000715255737,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.3540000021457672,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.118,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.699183884709573,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BP6_Moderate",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_005151.4",
"gene_symbol": "USP14",
"hgnc_id": 12612,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.17-3C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}