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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: 5-97167726-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=97167726&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 97167726,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_018343.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK2",
"gene_hgnc_id": 18999,
"hgvs_c": "c.1138A>G",
"hgvs_p": "p.Ser380Gly",
"transcript": "NM_018343.3",
"protein_id": "NP_060813.2",
"transcript_support_level": null,
"aa_start": 380,
"aa_end": null,
"aa_length": 552,
"cds_start": 1138,
"cds_end": null,
"cds_length": 1659,
"cdna_start": 1194,
"cdna_end": null,
"cdna_length": 3909,
"mane_select": "ENST00000283109.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK2",
"gene_hgnc_id": 18999,
"hgvs_c": "c.1138A>G",
"hgvs_p": "p.Ser380Gly",
"transcript": "ENST00000283109.8",
"protein_id": "ENSP00000283109.3",
"transcript_support_level": 1,
"aa_start": 380,
"aa_end": null,
"aa_length": 552,
"cds_start": 1138,
"cds_end": null,
"cds_length": 1659,
"cdna_start": 1194,
"cdna_end": null,
"cdna_length": 3909,
"mane_select": "NM_018343.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK2",
"gene_hgnc_id": 18999,
"hgvs_c": "c.1138A>G",
"hgvs_p": "p.Ser380Gly",
"transcript": "ENST00000508447.1",
"protein_id": "ENSP00000420932.1",
"transcript_support_level": 1,
"aa_start": 380,
"aa_end": null,
"aa_length": 474,
"cds_start": 1138,
"cds_end": null,
"cds_length": 1425,
"cdna_start": 1169,
"cdna_end": null,
"cdna_length": 2149,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK2",
"gene_hgnc_id": 18999,
"hgvs_c": "c.1138A>G",
"hgvs_p": "p.Ser380Gly",
"transcript": "NM_001159749.2",
"protein_id": "NP_001153221.1",
"transcript_support_level": null,
"aa_start": 380,
"aa_end": null,
"aa_length": 474,
"cds_start": 1138,
"cds_end": null,
"cds_length": 1425,
"cdna_start": 1194,
"cdna_end": null,
"cdna_length": 2174,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK2",
"gene_hgnc_id": 18999,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Ser193Gly",
"transcript": "XM_017009628.2",
"protein_id": "XP_016865117.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 365,
"cds_start": 577,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 817,
"cdna_end": null,
"cdna_length": 3532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LIX1-AS1",
"gene_hgnc_id": 52976,
"hgvs_c": "n.574-15282T>C",
"hgvs_p": null,
"transcript": "ENST00000504578.2",
"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": 1793,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK2",
"gene_hgnc_id": 18999,
"hgvs_c": "c.-150A>G",
"hgvs_p": null,
"transcript": "ENST00000511293.1",
"protein_id": "ENSP00000421830.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 158,
"cds_start": -4,
"cds_end": null,
"cds_length": 477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK2",
"gene_hgnc_id": 18999,
"hgvs_c": "c.-9A>G",
"hgvs_p": null,
"transcript": "ENST00000511012.1",
"protein_id": "ENSP00000422772.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 139,
"cds_start": -4,
"cds_end": null,
"cds_length": 420,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 442,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RIOK2",
"gene_hgnc_id": 18999,
"dbsnp": "rs191630960",
"frequency_reference_population": 0.000009912031,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.0000102612,
"gnomad_genomes_af": 0.00000656245,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.020432651042938232,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.096,
"revel_prediction": "Benign",
"alphamissense_score": 0.0606,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.903,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 4,
"pathogenic_score": 4,
"criteria": [
"PM1",
"PM2",
"BP4_Strong"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018343.3",
"gene_symbol": "RIOK2",
"hgnc_id": 18999,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1138A>G",
"hgvs_p": "p.Ser380Gly"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000504578.2",
"gene_symbol": "LIX1-AS1",
"hgnc_id": 52976,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.574-15282T>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}