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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: 5-103552248-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=103552248&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 103552248,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_031438.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT12",
"gene_hgnc_id": 18826,
"hgvs_c": "c.1247T>C",
"hgvs_p": "p.Ile416Thr",
"transcript": "NM_031438.4",
"protein_id": "NP_113626.1",
"transcript_support_level": null,
"aa_start": 416,
"aa_end": null,
"aa_length": 462,
"cds_start": 1247,
"cds_end": null,
"cds_length": 1389,
"cdna_start": 1340,
"cdna_end": null,
"cdna_length": 3488,
"mane_select": "ENST00000230792.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT12",
"gene_hgnc_id": 18826,
"hgvs_c": "c.1247T>C",
"hgvs_p": "p.Ile416Thr",
"transcript": "ENST00000230792.7",
"protein_id": "ENSP00000230792.2",
"transcript_support_level": 1,
"aa_start": 416,
"aa_end": null,
"aa_length": 462,
"cds_start": 1247,
"cds_end": null,
"cds_length": 1389,
"cdna_start": 1340,
"cdna_end": null,
"cdna_length": 3488,
"mane_select": "NM_031438.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT12",
"gene_hgnc_id": 18826,
"hgvs_c": "c.1193T>C",
"hgvs_p": "p.Ile398Thr",
"transcript": "NM_001300741.2",
"protein_id": "NP_001287670.1",
"transcript_support_level": null,
"aa_start": 398,
"aa_end": null,
"aa_length": 444,
"cds_start": 1193,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 1286,
"cdna_end": null,
"cdna_length": 3434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT12",
"gene_hgnc_id": 18826,
"hgvs_c": "c.1193T>C",
"hgvs_p": "p.Ile398Thr",
"transcript": "ENST00000507423.1",
"protein_id": "ENSP00000424521.1",
"transcript_support_level": 2,
"aa_start": 398,
"aa_end": null,
"aa_length": 444,
"cds_start": 1193,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 1286,
"cdna_end": null,
"cdna_length": 1781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT12",
"gene_hgnc_id": 18826,
"hgvs_c": "c.1247T>C",
"hgvs_p": "p.Ile416Thr",
"transcript": "XM_005272095.2",
"protein_id": "XP_005272152.1",
"transcript_support_level": null,
"aa_start": 416,
"aa_end": null,
"aa_length": 462,
"cds_start": 1247,
"cds_end": null,
"cds_length": 1389,
"cdna_start": 1336,
"cdna_end": null,
"cdna_length": 3484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT12",
"gene_hgnc_id": 18826,
"hgvs_c": "c.1193T>C",
"hgvs_p": "p.Ile398Thr",
"transcript": "XM_005272097.4",
"protein_id": "XP_005272154.1",
"transcript_support_level": null,
"aa_start": 398,
"aa_end": null,
"aa_length": 444,
"cds_start": 1193,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 1282,
"cdna_end": null,
"cdna_length": 3430,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000295164",
"gene_hgnc_id": null,
"hgvs_c": "n.93-151A>G",
"hgvs_p": null,
"transcript": "ENST00000728393.1",
"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": 343,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NUDT12",
"gene_hgnc_id": 18826,
"dbsnp": "rs773148354",
"frequency_reference_population": 0.000029126515,
"hom_count_reference_population": 0,
"allele_count_reference_population": 47,
"gnomad_exomes_af": 0.000030791,
"gnomad_genomes_af": 0.0000131418,
"gnomad_exomes_ac": 45,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8397024869918823,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.373,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7713,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.16,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.947,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.04,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_031438.4",
"gene_symbol": "NUDT12",
"hgnc_id": 18826,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1247T>C",
"hgvs_p": "p.Ile416Thr"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000728393.1",
"gene_symbol": "ENSG00000295164",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.93-151A>G",
"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
}