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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: 5-14690175-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=14690175&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 14690175,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000284274.5",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "c.731A>G",
"hgvs_p": "p.Tyr244Cys",
"transcript": "NM_138348.6",
"protein_id": "NP_612357.4",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 352,
"cds_start": 731,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 839,
"cdna_end": null,
"cdna_length": 7969,
"mane_select": "ENST00000284274.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "c.731A>G",
"hgvs_p": "p.Tyr244Cys",
"transcript": "ENST00000284274.5",
"protein_id": "ENSP00000284274.4",
"transcript_support_level": 1,
"aa_start": 244,
"aa_end": null,
"aa_length": 352,
"cds_start": 731,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 839,
"cdna_end": null,
"cdna_length": 7969,
"mane_select": "NM_138348.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "c.731A>G",
"hgvs_p": "p.Tyr244Cys",
"transcript": "ENST00000850613.1",
"protein_id": "ENSP00000520900.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 352,
"cds_start": 731,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 839,
"cdna_end": null,
"cdna_length": 5021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "c.731A>G",
"hgvs_p": "p.Tyr244Cys",
"transcript": "XM_011514151.3",
"protein_id": "XP_011512453.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 352,
"cds_start": 731,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 839,
"cdna_end": null,
"cdna_length": 5017,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "c.569A>G",
"hgvs_p": "p.Tyr190Cys",
"transcript": "XM_047417864.1",
"protein_id": "XP_047273820.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 298,
"cds_start": 569,
"cds_end": null,
"cds_length": 897,
"cdna_start": 717,
"cdna_end": null,
"cdna_length": 7847,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "c.476A>G",
"hgvs_p": "p.Tyr159Cys",
"transcript": "XM_017010015.2",
"protein_id": "XP_016865504.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 267,
"cds_start": 476,
"cds_end": null,
"cds_length": 804,
"cdna_start": 762,
"cdna_end": null,
"cdna_length": 7892,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "n.*477A>G",
"hgvs_p": null,
"transcript": "ENST00000503023.2",
"protein_id": "ENSP00000427016.1",
"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": 2924,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "n.*337A>G",
"hgvs_p": null,
"transcript": "ENST00000697367.1",
"protein_id": "ENSP00000513279.1",
"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": 2646,
"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": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "n.839A>G",
"hgvs_p": null,
"transcript": "XR_007058658.1",
"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": 5116,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "n.*477A>G",
"hgvs_p": null,
"transcript": "ENST00000503023.2",
"protein_id": "ENSP00000427016.1",
"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": 2924,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "n.*337A>G",
"hgvs_p": null,
"transcript": "ENST00000697367.1",
"protein_id": "ENSP00000513279.1",
"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": 2646,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "c.58-2679A>G",
"hgvs_p": null,
"transcript": "ENST00000506417.1",
"protein_id": "ENSP00000424966.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 83,
"cds_start": -4,
"cds_end": null,
"cds_length": 252,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 605,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "c.594+2529A>G",
"hgvs_p": null,
"transcript": "XM_011514154.3",
"protein_id": "XP_011512456.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 262,
"cds_start": -4,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7699,
"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": "OTULIN",
"gene_hgnc_id": 25118,
"hgvs_c": "n.*244A>G",
"hgvs_p": null,
"transcript": "ENST00000514913.1",
"protein_id": "ENSP00000421928.1",
"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": 420,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OTULIN",
"gene_hgnc_id": 25118,
"dbsnp": "rs886037887",
"frequency_reference_population": 6.8404694e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84047e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7842801809310913,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.398,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2312,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.13,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.297,
"phylop100way_prediction": "Uncertain_significance",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000284274.5",
"gene_symbol": "OTULIN",
"hgnc_id": 25118,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.731A>G",
"hgvs_p": "p.Tyr244Cys"
}
],
"clinvar_disease": " and dermatosis syndrome, autosomal recessive, panniculitis, susceptibility to invasive staphylococcus aureus infection,Autoinflammation,Immunodeficiency 107",
"clinvar_classification": " risk factor,Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Autoinflammation, panniculitis, and dermatosis syndrome, autosomal recessive|Immunodeficiency 107, susceptibility to invasive staphylococcus aureus infection",
"pathogenicity_classification_combined": "Pathogenic; risk factor",
"custom_annotations": null
}
],
"message": null
}