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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: 2-47373961-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=47373961&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "EPCAM",
"hgnc_id": 11529,
"hgvs_c": "c.338C>T",
"hgvs_p": "p.Thr113Ile",
"inheritance_mode": "AD,AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_002354.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_score": 2,
"allele_count_reference_population": 14,
"alphamissense_prediction": null,
"alphamissense_score": 0.8477,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.22,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Hereditary cancer-predisposing syndrome",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8412526249885559,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 314,
"aa_ref": "T",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1547,
"cdna_start": 533,
"cds_end": null,
"cds_length": 945,
"cds_start": 338,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_002354.3",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "c.338C>T",
"hgvs_p": "p.Thr113Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000263735.9",
"protein_coding": true,
"protein_id": "NP_002345.2",
"strand": true,
"transcript": "NM_002354.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 314,
"aa_ref": "T",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1547,
"cdna_start": 533,
"cds_end": null,
"cds_length": 945,
"cds_start": 338,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000263735.9",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "c.338C>T",
"hgvs_p": "p.Thr113Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002354.3",
"protein_coding": true,
"protein_id": "ENSP00000263735.4",
"strand": true,
"transcript": "ENST00000263735.9",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 342,
"aa_ref": "T",
"aa_start": 141,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1530,
"cdna_start": 636,
"cds_end": null,
"cds_length": 1029,
"cds_start": 422,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000405271.5",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "c.422C>T",
"hgvs_p": "p.Thr141Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000385476.1",
"strand": true,
"transcript": "ENST00000405271.5",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 324,
"aa_ref": "T",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1579,
"cdna_start": 535,
"cds_end": null,
"cds_length": 975,
"cds_start": 338,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000895681.1",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "c.338C>T",
"hgvs_p": "p.Thr113Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000565740.1",
"strand": true,
"transcript": "ENST00000895681.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 312,
"aa_ref": "T",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1439,
"cdna_start": 533,
"cds_end": null,
"cds_length": 939,
"cds_start": 338,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000895685.1",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "c.338C>T",
"hgvs_p": "p.Thr113Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000565744.1",
"strand": true,
"transcript": "ENST00000895685.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 289,
"aa_ref": "T",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1469,
"cdna_start": 533,
"cds_end": null,
"cds_length": 870,
"cds_start": 338,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000895683.1",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "c.338C>T",
"hgvs_p": "p.Thr113Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000565742.1",
"strand": true,
"transcript": "ENST00000895683.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 278,
"aa_ref": "T",
"aa_start": 77,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1439,
"cdna_start": 425,
"cds_end": null,
"cds_length": 837,
"cds_start": 230,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000934496.1",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "c.230C>T",
"hgvs_p": "p.Thr77Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604555.1",
"strand": true,
"transcript": "ENST00000934496.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 270,
"aa_ref": "T",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1415,
"cdna_start": 533,
"cds_end": null,
"cds_length": 813,
"cds_start": 338,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000895682.1",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "c.338C>T",
"hgvs_p": "p.Thr113Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000565741.1",
"strand": true,
"transcript": "ENST00000895682.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 247,
"aa_ref": "T",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1340,
"cdna_start": 531,
"cds_end": null,
"cds_length": 744,
"cds_start": 338,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000895684.1",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "c.338C>T",
"hgvs_p": "p.Thr113Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000565743.1",
"strand": true,
"transcript": "ENST00000895684.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 237,
"aa_ref": "T",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1376,
"cdna_start": 596,
"cds_end": null,
"cds_length": 714,
"cds_start": 338,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000934495.1",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "c.338C>T",
"hgvs_p": "p.Thr113Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604554.1",
"strand": true,
"transcript": "ENST00000934495.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 198,
"aa_ref": "T",
"aa_start": 189,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 609,
"cdna_start": 577,
"cds_end": null,
"cds_length": 598,
"cds_start": 566,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000419334.1",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "c.566C>T",
"hgvs_p": "p.Thr189Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000389028.1",
"strand": true,
"transcript": "ENST00000419334.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1501,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000456133.5",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "n.422C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000410675.1",
"strand": true,
"transcript": "ENST00000456133.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 714,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000474691.1",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "n.606C>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": "ENST00000474691.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 752,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000490733.1",
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"hgvs_c": "n.187C>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": "ENST00000490733.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs753947304",
"effect": "missense_variant",
"frequency_reference_population": 0.00000867437,
"gene_hgnc_id": 11529,
"gene_symbol": "EPCAM",
"gnomad_exomes_ac": 13,
"gnomad_exomes_af": 0.00000889276,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657523,
"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": "Hereditary cancer-predisposing syndrome",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.724,
"pos": 47373961,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.472,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_002354.3"
}
]
}