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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: 16-31110418-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=31110418&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 31110418,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000219794.11",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDK",
"gene_hgnc_id": 16902,
"hgvs_c": "c.561C>T",
"hgvs_p": "p.Arg187Arg",
"transcript": "NM_005881.4",
"protein_id": "NP_005872.2",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 412,
"cds_start": 561,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 832,
"cdna_end": null,
"cdna_length": 2036,
"mane_select": "ENST00000219794.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDK",
"gene_hgnc_id": 16902,
"hgvs_c": "c.561C>T",
"hgvs_p": "p.Arg187Arg",
"transcript": "ENST00000219794.11",
"protein_id": "ENSP00000219794.6",
"transcript_support_level": 1,
"aa_start": 187,
"aa_end": null,
"aa_length": 412,
"cds_start": 561,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 832,
"cdna_end": null,
"cdna_length": 2036,
"mane_select": "NM_005881.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDK",
"gene_hgnc_id": 16902,
"hgvs_c": "c.561C>T",
"hgvs_p": "p.Arg187Arg",
"transcript": "ENST00000287507.7",
"protein_id": "ENSP00000287507.3",
"transcript_support_level": 1,
"aa_start": 187,
"aa_end": null,
"aa_length": 335,
"cds_start": 561,
"cds_end": null,
"cds_length": 1008,
"cdna_start": 924,
"cdna_end": null,
"cdna_length": 1907,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDK",
"gene_hgnc_id": 16902,
"hgvs_c": "c.561C>T",
"hgvs_p": "p.Arg187Arg",
"transcript": "ENST00000394951.5",
"protein_id": "ENSP00000378405.1",
"transcript_support_level": 5,
"aa_start": 187,
"aa_end": null,
"aa_length": 412,
"cds_start": 561,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 1184,
"cdna_end": null,
"cdna_length": 2164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDK",
"gene_hgnc_id": 16902,
"hgvs_c": "c.561C>T",
"hgvs_p": "p.Arg187Arg",
"transcript": "NM_001122957.4",
"protein_id": "NP_001116429.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 365,
"cds_start": 561,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 832,
"cdna_end": null,
"cdna_length": 2176,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDK",
"gene_hgnc_id": 16902,
"hgvs_c": "c.561C>T",
"hgvs_p": "p.Arg187Arg",
"transcript": "ENST00000394950.7",
"protein_id": "ENSP00000378404.3",
"transcript_support_level": 2,
"aa_start": 187,
"aa_end": null,
"aa_length": 365,
"cds_start": 561,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 924,
"cdna_end": null,
"cdna_length": 1997,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDK",
"gene_hgnc_id": 16902,
"hgvs_c": "c.561C>T",
"hgvs_p": "p.Arg187Arg",
"transcript": "NM_001271926.3",
"protein_id": "NP_001258855.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 335,
"cds_start": 561,
"cds_end": null,
"cds_length": 1008,
"cdna_start": 832,
"cdna_end": null,
"cdna_length": 2086,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDK",
"gene_hgnc_id": 16902,
"hgvs_c": "c.534C>T",
"hgvs_p": "p.Arg178Arg",
"transcript": "ENST00000484226.2",
"protein_id": "ENSP00000457226.1",
"transcript_support_level": 3,
"aa_start": 178,
"aa_end": null,
"aa_length": 215,
"cds_start": 534,
"cds_end": null,
"cds_length": 650,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 754,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDK",
"gene_hgnc_id": 16902,
"hgvs_c": "c.561C>T",
"hgvs_p": "p.Arg187Arg",
"transcript": "XM_017022859.2",
"protein_id": "XP_016878348.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 410,
"cds_start": 561,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 832,
"cdna_end": null,
"cdna_length": 1543,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDK",
"gene_hgnc_id": 16902,
"hgvs_c": "n.1062C>T",
"hgvs_p": null,
"transcript": "ENST00000566568.1",
"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": 2558,
"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": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDK",
"gene_hgnc_id": 16902,
"hgvs_c": "n.561C>T",
"hgvs_p": null,
"transcript": "ENST00000567530.5",
"protein_id": "ENSP00000456479.1",
"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": 1796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BCKDK",
"gene_hgnc_id": 16902,
"dbsnp": "rs758510551",
"frequency_reference_population": 0.0000027365659,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273657,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6299999952316284,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.623,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000219794.11",
"gene_symbol": "BCKDK",
"hgnc_id": 16902,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.561C>T",
"hgvs_p": "p.Arg187Arg"
}
],
"clinvar_disease": "Branched-chain keto acid dehydrogenase kinase deficiency",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Branched-chain keto acid dehydrogenase kinase deficiency",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}