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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: 5-14664879-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=14664879&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "OTULIN",
"hgnc_id": 25118,
"hgvs_c": "c.54C>G",
"hgvs_p": "p.Ala18Ala",
"inheritance_mode": "AD,AR",
"pathogenic_score": 2,
"score": -3,
"transcript": "NM_138348.6",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_score": -3,
"allele_count_reference_population": 3,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.78,
"chr": "5",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7799999713897705,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 352,
"aa_ref": "A",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7969,
"cdna_start": 162,
"cds_end": null,
"cds_length": 1059,
"cds_start": 54,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_138348.6",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "c.54C>G",
"hgvs_p": "p.Ala18Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000284274.5",
"protein_coding": true,
"protein_id": "NP_612357.4",
"strand": true,
"transcript": "NM_138348.6",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 352,
"aa_ref": "A",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7969,
"cdna_start": 162,
"cds_end": null,
"cds_length": 1059,
"cds_start": 54,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000284274.5",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "c.54C>G",
"hgvs_p": "p.Ala18Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_138348.6",
"protein_coding": true,
"protein_id": "ENSP00000284274.4",
"strand": true,
"transcript": "ENST00000284274.5",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 352,
"aa_ref": "A",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5021,
"cdna_start": 162,
"cds_end": null,
"cds_length": 1059,
"cds_start": 54,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000850613.1",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "c.54C>G",
"hgvs_p": "p.Ala18Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000520900.1",
"strand": true,
"transcript": "ENST00000850613.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 310,
"aa_ref": "A",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2836,
"cdna_start": 162,
"cds_end": null,
"cds_length": 933,
"cds_start": 54,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000881544.1",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "c.54C>G",
"hgvs_p": "p.Ala18Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551603.1",
"strand": true,
"transcript": "ENST00000881544.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 310,
"aa_ref": "A",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4949,
"cdna_start": 216,
"cds_end": null,
"cds_length": 933,
"cds_start": 54,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000921417.1",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "c.54C>G",
"hgvs_p": "p.Ala18Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591476.1",
"strand": true,
"transcript": "ENST00000921417.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 262,
"aa_ref": "A",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6501,
"cdna_start": 209,
"cds_end": null,
"cds_length": 789,
"cds_start": 54,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000955678.1",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "c.54C>G",
"hgvs_p": "p.Ala18Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625737.1",
"strand": true,
"transcript": "ENST00000955678.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 352,
"aa_ref": "A",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5017,
"cdna_start": 162,
"cds_end": null,
"cds_length": 1059,
"cds_start": 54,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_011514151.3",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "c.54C>G",
"hgvs_p": "p.Ala18Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512453.1",
"strand": true,
"transcript": "XM_011514151.3",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 262,
"aa_ref": "A",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7699,
"cdna_start": 162,
"cds_end": null,
"cds_length": 789,
"cds_start": 54,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_011514154.3",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "c.54C>G",
"hgvs_p": "p.Ala18Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512456.1",
"strand": true,
"transcript": "XM_011514154.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 267,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7892,
"cdna_start": null,
"cds_end": null,
"cds_length": 804,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_017010015.2",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "c.-125C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016865504.1",
"strand": true,
"transcript": "XM_017010015.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2924,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000503023.2",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "n.54C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000427016.1",
"strand": true,
"transcript": "ENST00000503023.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 742,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000507335.1",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "n.148C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000507335.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2646,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000697367.1",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "n.54C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513279.1",
"strand": true,
"transcript": "ENST00000697367.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 5116,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XR_007058658.1",
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"hgvs_c": "n.162C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007058658.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs139848059",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0000028767045,
"gene_hgnc_id": 25118,
"gene_symbol": "OTULIN",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.0000028767,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -2.821,
"pos": 14664879,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_138348.6"
}
]
}