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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: 10-96595629-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=96595629&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 96595629,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_152309.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"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.2366C>T",
"hgvs_p": "p.Pro789Leu",
"transcript": "NM_152309.3",
"protein_id": "NP_689522.2",
"transcript_support_level": null,
"aa_start": 789,
"aa_end": null,
"aa_length": 805,
"cds_start": 2366,
"cds_end": null,
"cds_length": 2418,
"cdna_start": 2486,
"cdna_end": null,
"cdna_length": 4800,
"mane_select": "ENST00000339364.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"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.2366C>T",
"hgvs_p": "p.Pro789Leu",
"transcript": "ENST00000339364.10",
"protein_id": "ENSP00000339826.5",
"transcript_support_level": 1,
"aa_start": 789,
"aa_end": null,
"aa_length": 805,
"cds_start": 2366,
"cds_end": null,
"cds_length": 2418,
"cdna_start": 2486,
"cdna_end": null,
"cdna_length": 4800,
"mane_select": "NM_152309.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"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.1163C>T",
"hgvs_p": "p.Pro388Leu",
"transcript": "ENST00000371109.3",
"protein_id": "ENSP00000360150.3",
"transcript_support_level": 1,
"aa_start": 388,
"aa_end": null,
"aa_length": 404,
"cds_start": 1163,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 1345,
"cdna_end": null,
"cdna_length": 1766,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"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.1832C>T",
"hgvs_p": "p.Pro611Leu",
"transcript": "ENST00000371110.6",
"protein_id": "ENSP00000360151.2",
"transcript_support_level": 2,
"aa_start": 611,
"aa_end": null,
"aa_length": 627,
"cds_start": 1832,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 2017,
"cdna_end": null,
"cdna_length": 3151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"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.1832C>T",
"hgvs_p": "p.Pro611Leu",
"transcript": "XM_005269499.2",
"protein_id": "XP_005269556.1",
"transcript_support_level": null,
"aa_start": 611,
"aa_end": null,
"aa_length": 627,
"cds_start": 1832,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 1978,
"cdna_end": null,
"cdna_length": 4292,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"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.1832C>T",
"hgvs_p": "p.Pro611Leu",
"transcript": "XM_047424566.1",
"protein_id": "XP_047280522.1",
"transcript_support_level": null,
"aa_start": 611,
"aa_end": null,
"aa_length": 627,
"cds_start": 1832,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 2567,
"cdna_end": null,
"cdna_length": 4881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"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.2247C>T",
"hgvs_p": "p.Ser749Ser",
"transcript": "XM_011539248.2",
"protein_id": "XP_011537550.1",
"transcript_support_level": null,
"aa_start": 749,
"aa_end": null,
"aa_length": 796,
"cds_start": 2247,
"cds_end": null,
"cds_length": 2391,
"cdna_start": 2367,
"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.563C>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+4045G>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": "rs1261866966",
"frequency_reference_population": 0.0000086792,
"hom_count_reference_population": 0,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.00000616088,
"gnomad_genomes_af": 0.0000328468,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0400826632976532,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.041,
"revel_prediction": "Benign",
"alphamissense_score": 0.0626,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.65,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.908,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_152309.3",
"gene_symbol": "PIK3AP1",
"hgnc_id": 30034,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2366C>T",
"hgvs_p": "p.Pro789Leu"
},
{
"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+4045G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Infantile spasms,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Infantile spasms|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}