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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: 12-80670365-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=80670365&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 80670365,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000644991.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"hgvs_c": "c.6475C>A",
"hgvs_p": "p.Arg2159Arg",
"transcript": "NM_001145026.2",
"protein_id": "NP_001138498.1",
"transcript_support_level": null,
"aa_start": 2159,
"aa_end": null,
"aa_length": 2299,
"cds_start": 6475,
"cds_end": null,
"cds_length": 6900,
"cdna_start": 6586,
"cdna_end": null,
"cdna_length": 8261,
"mane_select": "ENST00000644991.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"hgvs_c": "c.6475C>A",
"hgvs_p": "p.Arg2159Arg",
"transcript": "ENST00000644991.3",
"protein_id": "ENSP00000495607.1",
"transcript_support_level": null,
"aa_start": 2159,
"aa_end": null,
"aa_length": 2299,
"cds_start": 6475,
"cds_end": null,
"cds_length": 6900,
"cdna_start": 6586,
"cdna_end": null,
"cdna_length": 8261,
"mane_select": "NM_001145026.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"hgvs_c": "c.6574C>A",
"hgvs_p": "p.Arg2192Arg",
"transcript": "ENST00000616559.4",
"protein_id": "ENSP00000483259.1",
"transcript_support_level": 5,
"aa_start": 2192,
"aa_end": null,
"aa_length": 2332,
"cds_start": 6574,
"cds_end": null,
"cds_length": 6999,
"cdna_start": 6574,
"cdna_end": null,
"cdna_length": 8165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000304204",
"gene_hgnc_id": null,
"hgvs_c": "n.100+36744G>T",
"hgvs_p": null,
"transcript": "ENST00000801015.1",
"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": 303,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000304204",
"gene_hgnc_id": null,
"hgvs_c": "n.101-18014G>T",
"hgvs_p": null,
"transcript": "ENST00000801016.1",
"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": 348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC105369867",
"gene_hgnc_id": null,
"hgvs_c": "n.130+36744G>T",
"hgvs_p": null,
"transcript": "XR_007063388.1",
"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": 2420,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPRQ",
"gene_hgnc_id": 9679,
"dbsnp": "rs1445287184",
"frequency_reference_population": 7.1499767e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.14998e-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": 0.04800000041723251,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.6700000166893005,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": 0.048,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.939,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.67,
"spliceai_max_prediction": "Pathogenic",
"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": "ENST00000644991.3",
"gene_symbol": "PTPRQ",
"hgnc_id": 9679,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,SD,AD,Unknown",
"hgvs_c": "c.6475C>A",
"hgvs_p": "p.Arg2159Arg"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000801015.1",
"gene_symbol": "ENSG00000304204",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.100+36744G>T",
"hgvs_p": null
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007063388.1",
"gene_symbol": "LOC105369867",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.130+36744G>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}