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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: 16-13948251-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=13948251&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 13948251,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000311895.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "c.2655G>A",
"hgvs_p": "p.Thr885Thr",
"transcript": "NM_005236.3",
"protein_id": "NP_005227.1",
"transcript_support_level": null,
"aa_start": 885,
"aa_end": null,
"aa_length": 916,
"cds_start": 2655,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 2667,
"cdna_end": null,
"cdna_length": 6764,
"mane_select": "ENST00000311895.8",
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "c.2655G>A",
"hgvs_p": "p.Thr885Thr",
"transcript": "ENST00000311895.8",
"protein_id": "ENSP00000310520.7",
"transcript_support_level": 1,
"aa_start": 885,
"aa_end": null,
"aa_length": 916,
"cds_start": 2655,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 2667,
"cdna_end": null,
"cdna_length": 6764,
"mane_select": "NM_005236.3",
"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": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "c.2793G>A",
"hgvs_p": "p.Thr931Thr",
"transcript": "ENST00000682617.1",
"protein_id": "ENSP00000507912.1",
"transcript_support_level": null,
"aa_start": 931,
"aa_end": null,
"aa_length": 962,
"cds_start": 2793,
"cds_end": null,
"cds_length": 2889,
"cdna_start": 2821,
"cdna_end": null,
"cdna_length": 6918,
"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": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "c.2793G>A",
"hgvs_p": "p.Thr931Thr",
"transcript": "XM_011522424.4",
"protein_id": "XP_011520726.1",
"transcript_support_level": null,
"aa_start": 931,
"aa_end": null,
"aa_length": 962,
"cds_start": 2793,
"cds_end": null,
"cds_length": 2889,
"cdna_start": 2805,
"cdna_end": null,
"cdna_length": 6902,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "c.1866G>A",
"hgvs_p": "p.Thr622Thr",
"transcript": "XM_047433774.1",
"protein_id": "XP_047289730.1",
"transcript_support_level": null,
"aa_start": 622,
"aa_end": null,
"aa_length": 653,
"cds_start": 1866,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 2011,
"cdna_end": null,
"cdna_length": 6108,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "c.1305G>A",
"hgvs_p": "p.Thr435Thr",
"transcript": "XM_011522427.2",
"protein_id": "XP_011520729.1",
"transcript_support_level": null,
"aa_start": 435,
"aa_end": null,
"aa_length": 466,
"cds_start": 1305,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 1642,
"cdna_end": null,
"cdna_length": 5739,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.1932G>A",
"hgvs_p": null,
"transcript": "ENST00000389138.7",
"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": 2106,
"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": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.*2349G>A",
"hgvs_p": null,
"transcript": "ENST00000683962.1",
"protein_id": "ENSP00000506854.1",
"transcript_support_level": null,
"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": 3925,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.*2349G>A",
"hgvs_p": null,
"transcript": "ENST00000683962.1",
"protein_id": "ENSP00000506854.1",
"transcript_support_level": null,
"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": 3925,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.*860G>A",
"hgvs_p": null,
"transcript": "ENST00000462862.1",
"protein_id": "ENSP00000461322.1",
"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": 721,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"dbsnp": "rs16963255",
"frequency_reference_population": 0.012665819,
"hom_count_reference_population": 193,
"allele_count_reference_population": 20444,
"gnomad_exomes_af": 0.0129478,
"gnomad_genomes_af": 0.00995783,
"gnomad_exomes_ac": 18928,
"gnomad_genomes_ac": 1516,
"gnomad_exomes_homalt": 181,
"gnomad_genomes_homalt": 12,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8199999928474426,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.82,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.79,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000311895.8",
"gene_symbol": "ERCC4",
"hgnc_id": 3436,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2655G>A",
"hgvs_p": "p.Thr885Thr"
}
],
"clinvar_disease": " group F,Cockayne syndrome,Fanconi anemia complementation group Q,XFE progeroid syndrome,Xeroderma pigmentosum,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:8",
"phenotype_combined": "not specified|Xeroderma pigmentosum, group F|Cockayne syndrome;Fanconi anemia complementation group Q;Xeroderma pigmentosum, group F|not provided|XFE progeroid syndrome;Fanconi anemia complementation group Q;Xeroderma pigmentosum, group F",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}