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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: 3-108552299-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=108552299&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 108552299,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_020890.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIP2A",
"gene_hgnc_id": 29302,
"hgvs_c": "c.2482A>G",
"hgvs_p": "p.Thr828Ala",
"transcript": "NM_020890.3",
"protein_id": "NP_065941.2",
"transcript_support_level": null,
"aa_start": 828,
"aa_end": null,
"aa_length": 905,
"cds_start": 2482,
"cds_end": null,
"cds_length": 2718,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000295746.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020890.3"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIP2A",
"gene_hgnc_id": 29302,
"hgvs_c": "c.2482A>G",
"hgvs_p": "p.Thr828Ala",
"transcript": "ENST00000295746.13",
"protein_id": "ENSP00000295746.7",
"transcript_support_level": 1,
"aa_start": 828,
"aa_end": null,
"aa_length": 905,
"cds_start": 2482,
"cds_end": null,
"cds_length": 2718,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020890.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295746.13"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIP2A",
"gene_hgnc_id": 29302,
"hgvs_c": "c.2005A>G",
"hgvs_p": "p.Thr669Ala",
"transcript": "ENST00000491772.5",
"protein_id": "ENSP00000419487.1",
"transcript_support_level": 1,
"aa_start": 669,
"aa_end": null,
"aa_length": 746,
"cds_start": 2005,
"cds_end": null,
"cds_length": 2241,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000491772.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIP2A",
"gene_hgnc_id": 29302,
"hgvs_c": "n.*2052A>G",
"hgvs_p": null,
"transcript": "ENST00000481530.5",
"protein_id": "ENSP00000417297.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000481530.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIP2A",
"gene_hgnc_id": 29302,
"hgvs_c": "n.*2052A>G",
"hgvs_p": null,
"transcript": "ENST00000481530.5",
"protein_id": "ENSP00000417297.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000481530.5"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIP2A",
"gene_hgnc_id": 29302,
"hgvs_c": "c.2479A>G",
"hgvs_p": "p.Thr827Ala",
"transcript": "ENST00000923233.1",
"protein_id": "ENSP00000593292.1",
"transcript_support_level": null,
"aa_start": 827,
"aa_end": null,
"aa_length": 904,
"cds_start": 2479,
"cds_end": null,
"cds_length": 2715,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923233.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIP2A",
"gene_hgnc_id": 29302,
"hgvs_c": "c.2479A>G",
"hgvs_p": "p.Thr827Ala",
"transcript": "XM_006713716.4",
"protein_id": "XP_006713779.1",
"transcript_support_level": null,
"aa_start": 827,
"aa_end": null,
"aa_length": 904,
"cds_start": 2479,
"cds_end": null,
"cds_length": 2715,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006713716.4"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIP2A",
"gene_hgnc_id": 29302,
"hgvs_c": "c.1540A>G",
"hgvs_p": "p.Thr514Ala",
"transcript": "XM_011513057.3",
"protein_id": "XP_011511359.1",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 591,
"cds_start": 1540,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513057.3"
}
],
"gene_symbol": "CIP2A",
"gene_hgnc_id": 29302,
"dbsnp": "rs777271322",
"frequency_reference_population": 0.0000070107635,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000635209,
"gnomad_genomes_af": 0.0000131441,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.018806159496307373,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.072,
"revel_prediction": "Benign",
"alphamissense_score": 0.0682,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.528,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_020890.3",
"gene_symbol": "CIP2A",
"hgnc_id": 29302,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2482A>G",
"hgvs_p": "p.Thr828Ala"
}
],
"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
}