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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: 10-96595626-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=96595626&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 96595626,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_152309.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3AP1",
"gene_hgnc_id": 30034,
"hgvs_c": "c.2369C>T",
"hgvs_p": "p.Thr790Ile",
"transcript": "NM_152309.3",
"protein_id": "NP_689522.2",
"transcript_support_level": null,
"aa_start": 790,
"aa_end": null,
"aa_length": 805,
"cds_start": 2369,
"cds_end": null,
"cds_length": 2418,
"cdna_start": 2489,
"cdna_end": null,
"cdna_length": 4800,
"mane_select": "ENST00000339364.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3AP1",
"gene_hgnc_id": 30034,
"hgvs_c": "c.2369C>T",
"hgvs_p": "p.Thr790Ile",
"transcript": "ENST00000339364.10",
"protein_id": "ENSP00000339826.5",
"transcript_support_level": 1,
"aa_start": 790,
"aa_end": null,
"aa_length": 805,
"cds_start": 2369,
"cds_end": null,
"cds_length": 2418,
"cdna_start": 2489,
"cdna_end": null,
"cdna_length": 4800,
"mane_select": "NM_152309.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3AP1",
"gene_hgnc_id": 30034,
"hgvs_c": "c.1166C>T",
"hgvs_p": "p.Thr389Ile",
"transcript": "ENST00000371109.3",
"protein_id": "ENSP00000360150.3",
"transcript_support_level": 1,
"aa_start": 389,
"aa_end": null,
"aa_length": 404,
"cds_start": 1166,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 1348,
"cdna_end": null,
"cdna_length": 1766,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3AP1",
"gene_hgnc_id": 30034,
"hgvs_c": "c.1835C>T",
"hgvs_p": "p.Thr612Ile",
"transcript": "ENST00000371110.6",
"protein_id": "ENSP00000360151.2",
"transcript_support_level": 2,
"aa_start": 612,
"aa_end": null,
"aa_length": 627,
"cds_start": 1835,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 2020,
"cdna_end": null,
"cdna_length": 3151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3AP1",
"gene_hgnc_id": 30034,
"hgvs_c": "c.1835C>T",
"hgvs_p": "p.Thr612Ile",
"transcript": "XM_005269499.2",
"protein_id": "XP_005269556.1",
"transcript_support_level": null,
"aa_start": 612,
"aa_end": null,
"aa_length": 627,
"cds_start": 1835,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 1981,
"cdna_end": null,
"cdna_length": 4292,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3AP1",
"gene_hgnc_id": 30034,
"hgvs_c": "c.1835C>T",
"hgvs_p": "p.Thr612Ile",
"transcript": "XM_047424566.1",
"protein_id": "XP_047280522.1",
"transcript_support_level": null,
"aa_start": 612,
"aa_end": null,
"aa_length": 627,
"cds_start": 1835,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 2570,
"cdna_end": null,
"cdna_length": 4881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3AP1",
"gene_hgnc_id": 30034,
"hgvs_c": "c.2250C>T",
"hgvs_p": "p.Asp750Asp",
"transcript": "XM_011539248.2",
"protein_id": "XP_011537550.1",
"transcript_support_level": null,
"aa_start": 750,
"aa_end": null,
"aa_length": 796,
"cds_start": 2250,
"cds_end": null,
"cds_length": 2391,
"cdna_start": 2370,
"cdna_end": null,
"cdna_length": 4681,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3AP1",
"gene_hgnc_id": 30034,
"hgvs_c": "n.566C>T",
"hgvs_p": null,
"transcript": "ENST00000467625.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 627,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC105378443",
"gene_hgnc_id": null,
"hgvs_c": "n.1446+4042G>A",
"hgvs_p": null,
"transcript": "XR_946220.4",
"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": 1535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PIK3AP1",
"gene_hgnc_id": 30034,
"dbsnp": "rs1334720195",
"frequency_reference_population": 0.0000018598238,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 6.84507e-7,
"gnomad_genomes_af": 0.0000131449,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06797698140144348,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.02,
"revel_prediction": "Benign",
"alphamissense_score": 0.1006,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.027,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_152309.3",
"gene_symbol": "PIK3AP1",
"hgnc_id": 30034,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2369C>T",
"hgvs_p": "p.Thr790Ile"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "XR_946220.4",
"gene_symbol": "LOC105378443",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1446+4042G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Infantile spasms",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Infantile spasms",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}