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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: 17-9645880-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=9645880&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "USP43",
"hgnc_id": 20072,
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_153210.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"downstream_gene_variant"
],
"gene_symbol": "LOC107985011",
"hgnc_id": null,
"hgvs_c": "n.*225G>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "XR_001752790.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 6,
"alphamissense_prediction": null,
"alphamissense_score": 0.0803,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.71,
"chr": "17",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.12664058804512024,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1123,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4185,
"cdna_start": 364,
"cds_end": null,
"cds_length": 3372,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_153210.5",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000285199.12",
"protein_coding": true,
"protein_id": "NP_694942.3",
"strand": true,
"transcript": "NM_153210.5",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1123,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4185,
"cdna_start": 364,
"cds_end": null,
"cds_length": 3372,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000285199.12",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_153210.5",
"protein_coding": true,
"protein_id": "ENSP00000285199.6",
"strand": true,
"transcript": "ENST00000285199.12",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1118,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3500,
"cdna_start": 344,
"cds_end": null,
"cds_length": 3357,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000570475.5",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000458963.1",
"strand": true,
"transcript": "ENST00000570475.5",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1126,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5050,
"cdna_start": 1218,
"cds_end": null,
"cds_length": 3381,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000936734.1",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606793.1",
"strand": true,
"transcript": "ENST00000936734.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1118,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4170,
"cdna_start": 364,
"cds_end": null,
"cds_length": 3357,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001267576.2",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001254505.1",
"strand": true,
"transcript": "NM_001267576.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1092,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4092,
"cdna_start": 364,
"cds_end": null,
"cds_length": 3279,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000902328.1",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572387.1",
"strand": true,
"transcript": "ENST00000902328.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1090,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4054,
"cdna_start": 336,
"cds_end": null,
"cds_length": 3273,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000902329.1",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572388.1",
"strand": true,
"transcript": "ENST00000902329.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1087,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4110,
"cdna_start": 393,
"cds_end": null,
"cds_length": 3264,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000936735.1",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606794.1",
"strand": true,
"transcript": "ENST00000936735.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1070,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4008,
"cdna_start": 340,
"cds_end": null,
"cds_length": 3213,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000936737.1",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606796.1",
"strand": true,
"transcript": "ENST00000936737.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1012,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3277,
"cdna_start": 366,
"cds_end": null,
"cds_length": 3039,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000936738.1",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606797.1",
"strand": true,
"transcript": "ENST00000936738.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1007,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3837,
"cdna_start": 364,
"cds_end": null,
"cds_length": 3024,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000936736.1",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606795.1",
"strand": true,
"transcript": "ENST00000936736.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1092,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4092,
"cdna_start": 364,
"cds_end": null,
"cds_length": 3279,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_011523639.3",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011521941.1",
"strand": true,
"transcript": "XM_011523639.3",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 703,
"aa_ref": "P",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2326,
"cdna_start": 364,
"cds_end": null,
"cds_length": 2112,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_047435320.1",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.248C>A",
"hgvs_p": "p.Pro83His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047291276.1",
"strand": true,
"transcript": "XM_047435320.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 920,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3544,
"cdna_start": null,
"cds_end": null,
"cds_length": 2763,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017024159.3",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.-2+538C>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016879648.1",
"strand": true,
"transcript": "XM_017024159.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 915,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3529,
"cdna_start": null,
"cds_end": null,
"cds_length": 2748,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047435319.1",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "c.-2+538C>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047291275.1",
"strand": true,
"transcript": "XM_047435319.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3624,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000570827.6",
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"hgvs_c": "n.645+538C>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000570827.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2931,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_001752790.2",
"gene_hgnc_id": null,
"gene_symbol": "LOC107985011",
"hgvs_c": "n.*225G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_001752790.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs958594387",
"effect": "missense_variant",
"frequency_reference_population": 0.0000041462695,
"gene_hgnc_id": 20072,
"gene_symbol": "USP43",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.00000308887,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131484,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.014,
"pos": 9645880,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.072,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_153210.5"
}
]
}