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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: 3-133616943-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=133616943&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 133616943,
"ref": "C",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000260810.10",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "TOPBP1",
"gene_hgnc_id": 17008,
"hgvs_c": "c.3760-18G>T",
"hgvs_p": null,
"transcript": "NM_007027.4",
"protein_id": "NP_008958.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1522,
"cds_start": -4,
"cds_end": null,
"cds_length": 4569,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5761,
"mane_select": "ENST00000260810.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "TOPBP1",
"gene_hgnc_id": 17008,
"hgvs_c": "c.3760-18G>T",
"hgvs_p": null,
"transcript": "ENST00000260810.10",
"protein_id": "ENSP00000260810.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1522,
"cds_start": -4,
"cds_end": null,
"cds_length": 4569,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5761,
"mane_select": "NM_007027.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "TOPBP1",
"gene_hgnc_id": 17008,
"hgvs_c": "c.3745-18G>T",
"hgvs_p": null,
"transcript": "NM_001363889.2",
"protein_id": "NP_001350818.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1517,
"cds_start": -4,
"cds_end": null,
"cds_length": 4554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "TOPBP1",
"gene_hgnc_id": 17008,
"hgvs_c": "c.3745-18G>T",
"hgvs_p": null,
"transcript": "ENST00000642236.1",
"protein_id": "ENSP00000493612.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1517,
"cds_start": -4,
"cds_end": null,
"cds_length": 4554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6152,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TOPBP1",
"gene_hgnc_id": 17008,
"hgvs_c": "n.368-18G>T",
"hgvs_p": null,
"transcript": "ENST00000505804.1",
"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": 472,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "TOPBP1",
"gene_hgnc_id": 17008,
"hgvs_c": "c.3760-18G>T",
"hgvs_p": null,
"transcript": "XM_017005636.3",
"protein_id": "XP_016861125.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1522,
"cds_start": -4,
"cds_end": null,
"cds_length": 4569,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5756,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "TOPBP1",
"gene_hgnc_id": 17008,
"hgvs_c": "c.3745-18G>T",
"hgvs_p": null,
"transcript": "XM_047447355.1",
"protein_id": "XP_047303311.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1517,
"cds_start": -4,
"cds_end": null,
"cds_length": 4554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5741,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOPBP1",
"gene_hgnc_id": 17008,
"hgvs_c": "c.*354G>T",
"hgvs_p": null,
"transcript": "XM_047447356.1",
"protein_id": "XP_047303312.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1183,
"cds_start": -4,
"cds_end": null,
"cds_length": 3552,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOPBP1",
"gene_hgnc_id": 17008,
"hgvs_c": "c.*354G>T",
"hgvs_p": null,
"transcript": "XM_047447357.1",
"protein_id": "XP_047303313.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1178,
"cds_start": -4,
"cds_end": null,
"cds_length": 3537,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOPBP1",
"gene_hgnc_id": 17008,
"hgvs_c": "c.*374G>T",
"hgvs_p": null,
"transcript": "XM_011512357.4",
"protein_id": "XP_011510659.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1126,
"cds_start": -4,
"cds_end": null,
"cds_length": 3381,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3718,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOPBP1",
"gene_hgnc_id": 17008,
"hgvs_c": "c.*374G>T",
"hgvs_p": null,
"transcript": "XM_047447358.1",
"protein_id": "XP_047303314.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1121,
"cds_start": -4,
"cds_end": null,
"cds_length": 3366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3703,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TOPBP1",
"gene_hgnc_id": 17008,
"dbsnp": "rs3732574",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4300000071525574,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.817,
"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": "ENST00000260810.10",
"gene_symbol": "TOPBP1",
"hgnc_id": 17008,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3760-18G>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}