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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: 12-117218154-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=117218154&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 117218154,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000620.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOS1",
"gene_hgnc_id": 7872,
"hgvs_c": "c.4181G>A",
"hgvs_p": "p.Arg1394Gln",
"transcript": "NM_000620.5",
"protein_id": "NP_000611.1",
"transcript_support_level": null,
"aa_start": 1394,
"aa_end": null,
"aa_length": 1434,
"cds_start": 4181,
"cds_end": null,
"cds_length": 4305,
"cdna_start": 4716,
"cdna_end": null,
"cdna_length": 12007,
"mane_select": "ENST00000317775.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOS1",
"gene_hgnc_id": 7872,
"hgvs_c": "c.4181G>A",
"hgvs_p": "p.Arg1394Gln",
"transcript": "ENST00000317775.11",
"protein_id": "ENSP00000320758.6",
"transcript_support_level": 1,
"aa_start": 1394,
"aa_end": null,
"aa_length": 1434,
"cds_start": 4181,
"cds_end": null,
"cds_length": 4305,
"cdna_start": 4716,
"cdna_end": null,
"cdna_length": 12007,
"mane_select": "NM_000620.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOS1",
"gene_hgnc_id": 7872,
"hgvs_c": "c.4283G>A",
"hgvs_p": "p.Arg1428Gln",
"transcript": "NM_001204218.2",
"protein_id": "NP_001191147.1",
"transcript_support_level": null,
"aa_start": 1428,
"aa_end": null,
"aa_length": 1468,
"cds_start": 4283,
"cds_end": null,
"cds_length": 4407,
"cdna_start": 4818,
"cdna_end": null,
"cdna_length": 12109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOS1",
"gene_hgnc_id": 7872,
"hgvs_c": "c.4283G>A",
"hgvs_p": "p.Arg1428Gln",
"transcript": "ENST00000338101.8",
"protein_id": "ENSP00000337459.4",
"transcript_support_level": 5,
"aa_start": 1428,
"aa_end": null,
"aa_length": 1468,
"cds_start": 4283,
"cds_end": null,
"cds_length": 4407,
"cdna_start": 4288,
"cdna_end": null,
"cdna_length": 4462,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOS1",
"gene_hgnc_id": 7872,
"hgvs_c": "c.4283G>A",
"hgvs_p": "p.Arg1428Gln",
"transcript": "ENST00000618760.4",
"protein_id": "ENSP00000477999.1",
"transcript_support_level": 5,
"aa_start": 1428,
"aa_end": null,
"aa_length": 1468,
"cds_start": 4283,
"cds_end": null,
"cds_length": 4407,
"cdna_start": 4994,
"cdna_end": null,
"cdna_length": 12283,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOS1",
"gene_hgnc_id": 7872,
"hgvs_c": "c.3173G>A",
"hgvs_p": "p.Arg1058Gln",
"transcript": "NM_001204213.2",
"protein_id": "NP_001191142.1",
"transcript_support_level": null,
"aa_start": 1058,
"aa_end": null,
"aa_length": 1098,
"cds_start": 3173,
"cds_end": null,
"cds_length": 3297,
"cdna_start": 3484,
"cdna_end": null,
"cdna_length": 10775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOS1",
"gene_hgnc_id": 7872,
"hgvs_c": "c.3173G>A",
"hgvs_p": "p.Arg1058Gln",
"transcript": "NM_001204214.2",
"protein_id": "NP_001191143.1",
"transcript_support_level": null,
"aa_start": 1058,
"aa_end": null,
"aa_length": 1098,
"cds_start": 3173,
"cds_end": null,
"cds_length": 3297,
"cdna_start": 3479,
"cdna_end": null,
"cdna_length": 10770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NOS1",
"gene_hgnc_id": 7872,
"dbsnp": "rs376113705",
"frequency_reference_population": 0.00015992264,
"hom_count_reference_population": 0,
"allele_count_reference_population": 258,
"gnomad_exomes_af": 0.000162213,
"gnomad_genomes_af": 0.000137938,
"gnomad_exomes_ac": 237,
"gnomad_genomes_ac": 21,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8087599873542786,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.86,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4724,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.38,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.515,
"phylop100way_prediction": "Uncertain_significance",
"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": "PP3",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000620.5",
"gene_symbol": "NOS1",
"hgnc_id": 7872,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4181G>A",
"hgvs_p": "p.Arg1394Gln"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "not provided",
"clinvar_review_status": "no classification provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "not provided",
"custom_annotations": null
}
],
"message": null
}