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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: 3-131381817-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=131381817&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 131381817,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001171906.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT16",
"gene_hgnc_id": 26442,
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Arg5Cys",
"transcript": "NM_152395.3",
"protein_id": "NP_689608.2",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 195,
"cds_start": 13,
"cds_end": null,
"cds_length": 588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000521288.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152395.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT16",
"gene_hgnc_id": 26442,
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Arg5Cys",
"transcript": "ENST00000521288.2",
"protein_id": "ENSP00000429274.2",
"transcript_support_level": 1,
"aa_start": 5,
"aa_end": null,
"aa_length": 195,
"cds_start": 13,
"cds_end": null,
"cds_length": 588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_152395.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000521288.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT16",
"gene_hgnc_id": 26442,
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Arg5Cys",
"transcript": "NM_001171906.2",
"protein_id": "NP_001165377.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 227,
"cds_start": 13,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001171906.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT16",
"gene_hgnc_id": 26442,
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Arg5Cys",
"transcript": "ENST00000502852.1",
"protein_id": "ENSP00000422375.1",
"transcript_support_level": 2,
"aa_start": 5,
"aa_end": null,
"aa_length": 227,
"cds_start": 13,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000502852.1"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NUDT16",
"gene_hgnc_id": 26442,
"hgvs_c": "c.-1+72C>T",
"hgvs_p": null,
"transcript": "NM_001171905.2",
"protein_id": "NP_001165376.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 159,
"cds_start": null,
"cds_end": null,
"cds_length": 480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001171905.2"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NUDT16",
"gene_hgnc_id": 26442,
"hgvs_c": "c.-1+72C>T",
"hgvs_p": null,
"transcript": "ENST00000537561.5",
"protein_id": "ENSP00000440230.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 159,
"cds_start": null,
"cds_end": null,
"cds_length": 480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000537561.5"
},
{
"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": "NUDT16",
"gene_hgnc_id": 26442,
"hgvs_c": "n.44C>T",
"hgvs_p": null,
"transcript": "NR_033268.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_033268.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"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": "NUDT16-DT",
"gene_hgnc_id": 27947,
"hgvs_c": "n.-161G>A",
"hgvs_p": null,
"transcript": "ENST00000660567.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000660567.1"
}
],
"gene_symbol": "NUDT16",
"gene_hgnc_id": 26442,
"dbsnp": "rs576393185",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.26468008756637573,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.113,
"revel_prediction": "Benign",
"alphamissense_score": 0.2643,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.139,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001171906.2",
"gene_symbol": "NUDT16",
"hgnc_id": 26442,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Arg5Cys"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000660567.1",
"gene_symbol": "NUDT16-DT",
"hgnc_id": 27947,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-161G>A",
"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
}