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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: 17-5133926-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=5133926&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 5133926,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004505.4",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "NM_001304284.2",
"protein_id": "NP_001291213.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 1406,
"cds_start": 424,
"cds_end": null,
"cds_length": 4221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000574788.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001304284.2"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "ENST00000574788.6",
"protein_id": "ENSP00000460380.1",
"transcript_support_level": 1,
"aa_start": 142,
"aa_end": null,
"aa_length": 1406,
"cds_start": 424,
"cds_end": null,
"cds_length": 4221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001304284.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000574788.6"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "ENST00000250066.6",
"protein_id": "ENSP00000250066.6",
"transcript_support_level": 1,
"aa_start": 142,
"aa_end": null,
"aa_length": 1406,
"cds_start": 424,
"cds_end": null,
"cds_length": 4221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000250066.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "n.870C>T",
"hgvs_p": null,
"transcript": "ENST00000357482.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000357482.5"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "NM_004505.4",
"protein_id": "NP_004496.2",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 1406,
"cds_start": 424,
"cds_end": null,
"cds_length": 4221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004505.4"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "XM_011524050.2",
"protein_id": "XP_011522352.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 1406,
"cds_start": 424,
"cds_end": null,
"cds_length": 4221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011524050.2"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "XM_011524051.3",
"protein_id": "XP_011522353.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 1406,
"cds_start": 424,
"cds_end": null,
"cds_length": 4221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011524051.3"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "XM_011524052.3",
"protein_id": "XP_011522354.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 1406,
"cds_start": 424,
"cds_end": null,
"cds_length": 4221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011524052.3"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "XM_011524053.3",
"protein_id": "XP_011522355.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 1406,
"cds_start": 424,
"cds_end": null,
"cds_length": 4221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011524053.3"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "XM_011524054.3",
"protein_id": "XP_011522356.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 1406,
"cds_start": 424,
"cds_end": null,
"cds_length": 4221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011524054.3"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "XM_011524055.3",
"protein_id": "XP_011522357.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 1406,
"cds_start": 424,
"cds_end": null,
"cds_length": 4221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011524055.3"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "XM_011524056.3",
"protein_id": "XP_011522358.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 1406,
"cds_start": 424,
"cds_end": null,
"cds_length": 4221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011524056.3"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "XM_047437018.1",
"protein_id": "XP_047292974.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 1384,
"cds_start": 424,
"cds_end": null,
"cds_length": 4155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437018.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "XM_011524058.3",
"protein_id": "XP_011522360.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 1031,
"cds_start": 424,
"cds_end": null,
"cds_length": 3096,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011524058.3"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr",
"transcript": "XM_011524059.3",
"protein_id": "XP_011522361.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 786,
"cds_start": 424,
"cds_end": null,
"cds_length": 2361,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011524059.3"
},
{
"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": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "n.424C>T",
"hgvs_p": null,
"transcript": "ENST00000572949.5",
"protein_id": "ENSP00000461581.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000572949.5"
},
{
"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": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "n.424C>T",
"hgvs_p": null,
"transcript": "ENST00000575709.5",
"protein_id": "ENSP00000461817.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000575709.5"
}
],
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"dbsnp": "rs773459780",
"frequency_reference_population": 0.000013009589,
"hom_count_reference_population": 0,
"allele_count_reference_population": 21,
"gnomad_exomes_af": 0.0000102608,
"gnomad_genomes_af": 0.0000393923,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.13034865260124207,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.068,
"revel_prediction": "Benign",
"alphamissense_score": 0.2159,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.443,
"phylop100way_prediction": "Benign",
"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": "NM_004505.4",
"gene_symbol": "USP6",
"hgnc_id": 12629,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.424C>T",
"hgvs_p": "p.His142Tyr"
}
],
"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
}