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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: 17-56844133-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=56844133&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 56844133,
"ref": "A",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000284061.8",
"consequences": [
{
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.579A>T",
"hgvs_p": "p.Thr193Thr",
"transcript": "NM_003647.3",
"protein_id": "NP_003638.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 567,
"cds_start": 579,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 707,
"cdna_end": null,
"cdna_length": 8608,
"mane_select": "ENST00000284061.8",
"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": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.579A>T",
"hgvs_p": "p.Thr193Thr",
"transcript": "ENST00000284061.8",
"protein_id": "ENSP00000284061.3",
"transcript_support_level": 1,
"aa_start": 193,
"aa_end": null,
"aa_length": 567,
"cds_start": 579,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 707,
"cdna_end": null,
"cdna_length": 8608,
"mane_select": "NM_003647.3",
"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": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.408A>T",
"hgvs_p": "p.Thr136Thr",
"transcript": "ENST00000572944.1",
"protein_id": "ENSP00000458493.1",
"transcript_support_level": 1,
"aa_start": 136,
"aa_end": null,
"aa_length": 455,
"cds_start": 408,
"cds_end": null,
"cds_length": 1368,
"cdna_start": 409,
"cdna_end": null,
"cdna_length": 5179,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "n.727A>T",
"hgvs_p": null,
"transcript": "ENST00000576869.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 1105,
"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": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.633A>T",
"hgvs_p": "p.Thr211Thr",
"transcript": "XM_047436959.1",
"protein_id": "XP_047292915.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 709,
"cds_start": 633,
"cds_end": null,
"cds_length": 2130,
"cdna_start": 952,
"cdna_end": null,
"cdna_length": 9225,
"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": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.579A>T",
"hgvs_p": "p.Thr193Thr",
"transcript": "XM_017025243.3",
"protein_id": "XP_016880732.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 691,
"cds_start": 579,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 707,
"cdna_end": null,
"cdna_length": 8980,
"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": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.633A>T",
"hgvs_p": "p.Thr211Thr",
"transcript": "XM_011525394.4",
"protein_id": "XP_011523696.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 585,
"cds_start": 633,
"cds_end": null,
"cds_length": 1758,
"cdna_start": 952,
"cdna_end": null,
"cdna_length": 8853,
"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": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.633A>T",
"hgvs_p": "p.Thr211Thr",
"transcript": "XM_017025244.3",
"protein_id": "XP_016880733.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 561,
"cds_start": 633,
"cds_end": null,
"cds_length": 1686,
"cdna_start": 952,
"cdna_end": null,
"cdna_length": 8781,
"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": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.633A>T",
"hgvs_p": "p.Thr211Thr",
"transcript": "XM_011525395.3",
"protein_id": "XP_011523697.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 543,
"cds_start": 633,
"cds_end": null,
"cds_length": 1632,
"cdna_start": 952,
"cdna_end": null,
"cdna_length": 2046,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.123A>T",
"hgvs_p": "p.Thr41Thr",
"transcript": "XM_047436960.1",
"protein_id": "XP_047292916.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 539,
"cds_start": 123,
"cds_end": null,
"cds_length": 1620,
"cdna_start": 201,
"cdna_end": null,
"cdna_length": 8474,
"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": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.633A>T",
"hgvs_p": "p.Thr211Thr",
"transcript": "XM_011525396.3",
"protein_id": "XP_011523698.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 452,
"cds_start": 633,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 952,
"cdna_end": null,
"cdna_length": 1781,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "n.115A>T",
"hgvs_p": null,
"transcript": "ENST00000571084.1",
"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": 773,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "n.952A>T",
"hgvs_p": null,
"transcript": "XR_002958079.2",
"protein_id": null,
"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": 1724,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "TRIM25",
"gene_hgnc_id": 12932,
"hgvs_c": "n.*314-343T>A",
"hgvs_p": null,
"transcript": "ENST00000648772.1",
"protein_id": "ENSP00000498158.1",
"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": 4248,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"dbsnp": "rs3760158",
"frequency_reference_population": 0.000019730092,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000211135,
"gnomad_genomes_af": 0.0000197301,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8899999856948853,
"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": -0.89,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.356,
"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": -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": "ENST00000284061.8",
"gene_symbol": "DGKE",
"hgnc_id": 2852,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.579A>T",
"hgvs_p": "p.Thr193Thr"
},
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000648772.1",
"gene_symbol": "TRIM25",
"hgnc_id": 12932,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.*314-343T>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}