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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: 3-179198856-TGGGGCATCCACTTGATGCCCC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=179198856&ref=TGGGGCATCCACTTGATGCCCC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 179198856,
"ref": "TGGGGCATCCACTTGATGCCCC",
"alt": "T",
"effect": "disruptive_inframe_deletion",
"transcript": "NM_006218.4",
"consequences": [
{
"aa_ref": "WGIHLMPP",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.32_52delGGGGCATCCACTTGATGCCCC",
"hgvs_p": "p.Trp11_Pro18delinsSer",
"transcript": "NM_006218.4",
"protein_id": "NP_006209.2",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 1068,
"cds_start": 32,
"cds_end": null,
"cds_length": 3207,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 9259,
"mane_select": "ENST00000263967.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "WGIHLMPP",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.32_52delGGGGCATCCACTTGATGCCCC",
"hgvs_p": "p.Trp11_Pro18delinsSer",
"transcript": "ENST00000263967.4",
"protein_id": "ENSP00000263967.3",
"transcript_support_level": 2,
"aa_start": 11,
"aa_end": null,
"aa_length": 1068,
"cds_start": 32,
"cds_end": null,
"cds_length": 3207,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 9259,
"mane_select": "NM_006218.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "WGIHLMPP",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.32_52delGGGGCATCCACTTGATGCCCC",
"hgvs_p": "p.Trp11_Pro18delinsSer",
"transcript": "ENST00000643187.1",
"protein_id": "ENSP00000493507.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 1000,
"cds_start": 32,
"cds_end": null,
"cds_length": 3003,
"cdna_start": 138,
"cdna_end": null,
"cdna_length": 4130,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "WGIHLMPP",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.32_52delGGGGCATCCACTTGATGCCCC",
"hgvs_p": "p.Trp11_Pro18delinsSer",
"transcript": "ENST00000468036.1",
"protein_id": "ENSP00000417479.1",
"transcript_support_level": 3,
"aa_start": 11,
"aa_end": null,
"aa_length": 117,
"cds_start": 32,
"cds_end": null,
"cds_length": 354,
"cdna_start": 298,
"cdna_end": null,
"cdna_length": 620,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "WGIHLMPP",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.32_52delGGGGCATCCACTTGATGCCCC",
"hgvs_p": "p.Trp11_Pro18delinsSer",
"transcript": "ENST00000477735.1",
"protein_id": "ENSP00000418145.1",
"transcript_support_level": 4,
"aa_start": 11,
"aa_end": null,
"aa_length": 20,
"cds_start": 32,
"cds_end": null,
"cds_length": 63,
"cdna_start": 214,
"cdna_end": null,
"cdna_length": 245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "WGIHLMPP",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.32_52delGGGGCATCCACTTGATGCCCC",
"hgvs_p": "p.Trp11_Pro18delinsSer",
"transcript": "XM_006713658.5",
"protein_id": "XP_006713721.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 1068,
"cds_start": 32,
"cds_end": null,
"cds_length": 3207,
"cdna_start": 202,
"cdna_end": null,
"cdna_length": 9106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "n.2839_2859delGGGGCATCCACTTGATGCCCC",
"hgvs_p": null,
"transcript": "ENST00000675467.1",
"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": 7021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "n.32_52delGGGGCATCCACTTGATGCCCC",
"hgvs_p": null,
"transcript": "ENST00000675786.1",
"protein_id": "ENSP00000502323.1",
"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": 4148,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"dbsnp": "rs2108385065",
"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": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.509,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM4,PP3,PP5_Moderate",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM4",
"PP3",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006218.4",
"gene_symbol": "PIK3CA",
"hgnc_id": 8975,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AD",
"hgvs_c": "c.32_52delGGGGCATCCACTTGATGCCCC",
"hgvs_p": "p.Trp11_Pro18delinsSer"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}