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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: 17-56835096-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=56835096&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 56835096,
"ref": "A",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000284061.8",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.301A>T",
"hgvs_p": "p.Lys101*",
"transcript": "NM_003647.3",
"protein_id": "NP_003638.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 567,
"cds_start": 301,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 429,
"cdna_end": null,
"cdna_length": 8608,
"mane_select": "ENST00000284061.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.301A>T",
"hgvs_p": "p.Lys101*",
"transcript": "ENST00000284061.8",
"protein_id": "ENSP00000284061.3",
"transcript_support_level": 1,
"aa_start": 101,
"aa_end": null,
"aa_length": 567,
"cds_start": 301,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 429,
"cdna_end": null,
"cdna_length": 8608,
"mane_select": "NM_003647.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.130A>T",
"hgvs_p": "p.Lys44*",
"transcript": "ENST00000572944.1",
"protein_id": "ENSP00000458493.1",
"transcript_support_level": 1,
"aa_start": 44,
"aa_end": null,
"aa_length": 455,
"cds_start": 130,
"cds_end": null,
"cds_length": 1368,
"cdna_start": 131,
"cdna_end": null,
"cdna_length": 5179,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.301A>T",
"hgvs_p": "p.Lys101*",
"transcript": "ENST00000572810.1",
"protein_id": "ENSP00000459295.1",
"transcript_support_level": 1,
"aa_start": 101,
"aa_end": null,
"aa_length": 177,
"cds_start": 301,
"cds_end": null,
"cds_length": 534,
"cdna_start": 473,
"cdna_end": null,
"cdna_length": 1843,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "n.449A>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": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.355A>T",
"hgvs_p": "p.Lys119*",
"transcript": "XM_047436959.1",
"protein_id": "XP_047292915.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 709,
"cds_start": 355,
"cds_end": null,
"cds_length": 2130,
"cdna_start": 674,
"cdna_end": null,
"cdna_length": 9225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.301A>T",
"hgvs_p": "p.Lys101*",
"transcript": "XM_017025243.3",
"protein_id": "XP_016880732.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 691,
"cds_start": 301,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 429,
"cdna_end": null,
"cdna_length": 8980,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.355A>T",
"hgvs_p": "p.Lys119*",
"transcript": "XM_011525394.4",
"protein_id": "XP_011523696.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 585,
"cds_start": 355,
"cds_end": null,
"cds_length": 1758,
"cdna_start": 674,
"cdna_end": null,
"cdna_length": 8853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"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.355A>T",
"hgvs_p": "p.Lys119*",
"transcript": "XM_017025244.3",
"protein_id": "XP_016880733.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 561,
"cds_start": 355,
"cds_end": null,
"cds_length": 1686,
"cdna_start": 674,
"cdna_end": null,
"cdna_length": 8781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "c.355A>T",
"hgvs_p": "p.Lys119*",
"transcript": "XM_011525395.3",
"protein_id": "XP_011523697.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 543,
"cds_start": 355,
"cds_end": null,
"cds_length": 1632,
"cdna_start": 674,
"cdna_end": null,
"cdna_length": 2046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"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.355A>T",
"hgvs_p": "p.Lys119*",
"transcript": "XM_011525396.3",
"protein_id": "XP_011523698.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 452,
"cds_start": 355,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 674,
"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": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"hgvs_c": "n.674A>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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "C17orf67",
"gene_hgnc_id": 27900,
"hgvs_c": "n.285+3393T>A",
"hgvs_p": null,
"transcript": "ENST00000487705.1",
"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": 633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DGKE",
"gene_hgnc_id": 2852,
"dbsnp": "rs777787526",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.550000011920929,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.8299999833106995,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.191,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.83,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PVS1",
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000284061.8",
"gene_symbol": "DGKE",
"hgnc_id": 2852,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.301A>T",
"hgvs_p": "p.Lys101*"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000487705.1",
"gene_symbol": "C17orf67",
"hgnc_id": 27900,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.285+3393T>A",
"hgvs_p": null
}
],
"clinvar_disease": "Atypical hemolytic-uremic syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Atypical hemolytic-uremic syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}