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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: 17-5132426-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=5132426&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 5132426,
"ref": "G",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000574788.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "NM_001304284.2",
"protein_id": "NP_001291213.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 1406,
"cds_start": 186,
"cds_end": null,
"cds_length": 4221,
"cdna_start": 2822,
"cdna_end": null,
"cdna_length": 8870,
"mane_select": "ENST00000574788.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "ENST00000574788.6",
"protein_id": "ENSP00000460380.1",
"transcript_support_level": 1,
"aa_start": 62,
"aa_end": null,
"aa_length": 1406,
"cds_start": 186,
"cds_end": null,
"cds_length": 4221,
"cdna_start": 2822,
"cdna_end": null,
"cdna_length": 8870,
"mane_select": "NM_001304284.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "ENST00000250066.6",
"protein_id": "ENSP00000250066.6",
"transcript_support_level": 1,
"aa_start": 62,
"aa_end": null,
"aa_length": 1406,
"cds_start": 186,
"cds_end": null,
"cds_length": 4221,
"cdna_start": 1885,
"cdna_end": null,
"cdna_length": 7976,
"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": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "n.632G>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "NM_004505.4",
"protein_id": "NP_004496.2",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 1406,
"cds_start": 186,
"cds_end": null,
"cds_length": 4221,
"cdna_start": 1468,
"cdna_end": null,
"cdna_length": 7516,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "XM_011524050.2",
"protein_id": "XP_011522352.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 1406,
"cds_start": 186,
"cds_end": null,
"cds_length": 4221,
"cdna_start": 2987,
"cdna_end": null,
"cdna_length": 9035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "XM_011524051.3",
"protein_id": "XP_011522353.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 1406,
"cds_start": 186,
"cds_end": null,
"cds_length": 4221,
"cdna_start": 2082,
"cdna_end": null,
"cdna_length": 8130,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "XM_011524052.3",
"protein_id": "XP_011522354.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 1406,
"cds_start": 186,
"cds_end": null,
"cds_length": 4221,
"cdna_start": 1834,
"cdna_end": null,
"cdna_length": 7882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "XM_011524053.3",
"protein_id": "XP_011522355.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 1406,
"cds_start": 186,
"cds_end": null,
"cds_length": 4221,
"cdna_start": 2109,
"cdna_end": null,
"cdna_length": 8157,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "XM_011524054.3",
"protein_id": "XP_011522356.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 1406,
"cds_start": 186,
"cds_end": null,
"cds_length": 4221,
"cdna_start": 2076,
"cdna_end": null,
"cdna_length": 8124,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "XM_011524055.3",
"protein_id": "XP_011522357.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 1406,
"cds_start": 186,
"cds_end": null,
"cds_length": 4221,
"cdna_start": 2003,
"cdna_end": null,
"cdna_length": 8051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "XM_011524056.3",
"protein_id": "XP_011522358.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 1406,
"cds_start": 186,
"cds_end": null,
"cds_length": 4221,
"cdna_start": 455,
"cdna_end": null,
"cdna_length": 6503,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "XM_047437018.1",
"protein_id": "XP_047292974.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 1384,
"cds_start": 186,
"cds_end": null,
"cds_length": 4155,
"cdna_start": 2987,
"cdna_end": null,
"cdna_length": 8969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "XM_011524058.3",
"protein_id": "XP_011522360.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 1031,
"cds_start": 186,
"cds_end": null,
"cds_length": 3096,
"cdna_start": 2193,
"cdna_end": null,
"cdna_length": 5118,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg",
"transcript": "XM_011524059.3",
"protein_id": "XP_011522361.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 786,
"cds_start": 186,
"cds_end": null,
"cds_length": 2361,
"cdna_start": 2204,
"cdna_end": null,
"cdna_length": 4474,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "n.371G>T",
"hgvs_p": null,
"transcript": "ENST00000572429.5",
"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": 569,
"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": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "n.186G>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7862,
"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": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"hgvs_c": "n.186G>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8185,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "USP6",
"gene_hgnc_id": 12629,
"dbsnp": "rs145160344",
"frequency_reference_population": 0.000006570216,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000657022,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7099999785423279,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.71,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.05,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000574788.6",
"gene_symbol": "USP6",
"hgnc_id": 12629,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.186G>T",
"hgvs_p": "p.Arg62Arg"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}