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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: 2-47373533-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=47373533&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 47373533,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000263735.9",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPCAM",
"gene_hgnc_id": 11529,
"hgvs_c": "c.147T>C",
"hgvs_p": "p.Thr49Thr",
"transcript": "NM_002354.3",
"protein_id": "NP_002345.2",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 314,
"cds_start": 147,
"cds_end": null,
"cds_length": 945,
"cdna_start": 342,
"cdna_end": null,
"cdna_length": 1547,
"mane_select": "ENST00000263735.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPCAM",
"gene_hgnc_id": 11529,
"hgvs_c": "c.147T>C",
"hgvs_p": "p.Thr49Thr",
"transcript": "ENST00000263735.9",
"protein_id": "ENSP00000263735.4",
"transcript_support_level": 1,
"aa_start": 49,
"aa_end": null,
"aa_length": 314,
"cds_start": 147,
"cds_end": null,
"cds_length": 945,
"cdna_start": 342,
"cdna_end": null,
"cdna_length": 1547,
"mane_select": "NM_002354.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPCAM",
"gene_hgnc_id": 11529,
"hgvs_c": "c.231T>C",
"hgvs_p": "p.Thr77Thr",
"transcript": "ENST00000405271.5",
"protein_id": "ENSP00000385476.1",
"transcript_support_level": 5,
"aa_start": 77,
"aa_end": null,
"aa_length": 342,
"cds_start": 231,
"cds_end": null,
"cds_length": 1029,
"cdna_start": 445,
"cdna_end": null,
"cdna_length": 1530,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPCAM",
"gene_hgnc_id": 11529,
"hgvs_c": "c.375T>C",
"hgvs_p": "p.Thr125Thr",
"transcript": "ENST00000419334.1",
"protein_id": "ENSP00000389028.1",
"transcript_support_level": 3,
"aa_start": 125,
"aa_end": null,
"aa_length": 198,
"cds_start": 375,
"cds_end": null,
"cds_length": 598,
"cdna_start": 386,
"cdna_end": null,
"cdna_length": 609,
"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": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPCAM",
"gene_hgnc_id": 11529,
"hgvs_c": "n.231T>C",
"hgvs_p": null,
"transcript": "ENST00000456133.5",
"protein_id": "ENSP00000410675.1",
"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": 1501,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPCAM",
"gene_hgnc_id": 11529,
"hgvs_c": "n.178T>C",
"hgvs_p": null,
"transcript": "ENST00000474691.1",
"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": 714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPCAM",
"gene_hgnc_id": 11529,
"hgvs_c": "n.-242T>C",
"hgvs_p": null,
"transcript": "ENST00000490733.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 752,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EPCAM",
"gene_hgnc_id": 11529,
"dbsnp": "rs190508047",
"frequency_reference_population": 0.000022307708,
"hom_count_reference_population": 0,
"allele_count_reference_population": 36,
"gnomad_exomes_af": 0.0000164217,
"gnomad_genomes_af": 0.0000787857,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 12,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8399999737739563,
"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": -0.84,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.229,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS1",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000263735.9",
"gene_symbol": "EPCAM",
"hgnc_id": 11529,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.147T>C",
"hgvs_p": "p.Thr49Thr"
}
],
"clinvar_disease": "Lynch syndrome,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Lynch syndrome|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}