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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: 16-92686-TG-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=92686&ref=TG&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 92686,
"ref": "TG",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "ENST00000611875.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.1070delC",
"hgvs_p": "p.Pro357fs",
"transcript": "NM_001077350.3",
"protein_id": "NP_001070818.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 569,
"cds_start": 1070,
"cds_end": null,
"cds_length": 1710,
"cdna_start": 1169,
"cdna_end": null,
"cdna_length": 3128,
"mane_select": "ENST00000611875.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.1070delC",
"hgvs_p": "p.Pro357fs",
"transcript": "ENST00000611875.5",
"protein_id": "ENSP00000478273.1",
"transcript_support_level": 5,
"aa_start": 357,
"aa_end": null,
"aa_length": 569,
"cds_start": 1070,
"cds_end": null,
"cds_length": 1710,
"cdna_start": 1169,
"cdna_end": null,
"cdna_length": 3128,
"mane_select": "NM_001077350.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.995delC",
"hgvs_p": "p.Pro332fs",
"transcript": "ENST00000399953.7",
"protein_id": "ENSP00000382834.4",
"transcript_support_level": 1,
"aa_start": 332,
"aa_end": null,
"aa_length": 544,
"cds_start": 995,
"cds_end": null,
"cds_length": 1635,
"cdna_start": 1240,
"cdna_end": null,
"cdna_length": 2784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "n.*655delC",
"hgvs_p": null,
"transcript": "ENST00000621703.4",
"protein_id": "ENSP00000477801.1",
"transcript_support_level": 1,
"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": 2812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "n.*655delC",
"hgvs_p": null,
"transcript": "ENST00000621703.4",
"protein_id": "ENSP00000477801.1",
"transcript_support_level": 1,
"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": 2812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.995delC",
"hgvs_p": "p.Pro332fs",
"transcript": "NM_001243248.2",
"protein_id": "NP_001230177.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 544,
"cds_start": 995,
"cds_end": null,
"cds_length": 1635,
"cdna_start": 1369,
"cdna_end": null,
"cdna_length": 3328,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.995delC",
"hgvs_p": "p.Pro332fs",
"transcript": "NM_001243249.2",
"protein_id": "NP_001230178.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 544,
"cds_start": 995,
"cds_end": null,
"cds_length": 1635,
"cdna_start": 1401,
"cdna_end": null,
"cdna_length": 3360,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.836delC",
"hgvs_p": "p.Pro279fs",
"transcript": "NM_001243247.2",
"protein_id": "NP_001230176.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 491,
"cds_start": 836,
"cds_end": null,
"cds_length": 1476,
"cdna_start": 1306,
"cdna_end": null,
"cdna_length": 3265,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "c.533delC",
"hgvs_p": "p.Pro178fs",
"transcript": "NM_001039476.3",
"protein_id": "NP_001034565.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 390,
"cds_start": 533,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 1271,
"cdna_end": null,
"cdna_length": 3230,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "n.*706delC",
"hgvs_p": null,
"transcript": "ENST00000622194.4",
"protein_id": "ENSP00000478045.1",
"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": 2981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "n.*706delC",
"hgvs_p": null,
"transcript": "ENST00000622194.4",
"protein_id": "ENSP00000478045.1",
"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": 2981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"hgvs_c": "n.*104delC",
"hgvs_p": null,
"transcript": "ENST00000464069.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NPRL3",
"gene_hgnc_id": 14124,
"dbsnp": "rs886037962",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 7.753,
"phylop100way_prediction": "Pathogenic",
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000611875.5",
"gene_symbol": "NPRL3",
"hgnc_id": 14124,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1070delC",
"hgvs_p": "p.Pro357fs"
}
],
"clinvar_disease": " familial focal, with variable foci 3,Epilepsy",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Epilepsy, familial focal, with variable foci 3",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}