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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: 3-179234297-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=179234297&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 179234297,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_006218.4",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.3140A>G",
"hgvs_p": "p.His1047Arg",
"transcript": "NM_006218.4",
"protein_id": "NP_006209.2",
"transcript_support_level": null,
"aa_start": 1047,
"aa_end": null,
"aa_length": 1068,
"cds_start": 3140,
"cds_end": null,
"cds_length": 3207,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000263967.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006218.4"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.3140A>G",
"hgvs_p": "p.His1047Arg",
"transcript": "ENST00000263967.4",
"protein_id": "ENSP00000263967.3",
"transcript_support_level": 2,
"aa_start": 1047,
"aa_end": null,
"aa_length": 1068,
"cds_start": 3140,
"cds_end": null,
"cds_length": 3207,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006218.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263967.4"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.3170A>G",
"hgvs_p": "p.His1057Arg",
"transcript": "ENST00000955190.1",
"protein_id": "ENSP00000625249.1",
"transcript_support_level": null,
"aa_start": 1057,
"aa_end": null,
"aa_length": 1078,
"cds_start": 3170,
"cds_end": null,
"cds_length": 3237,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955190.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.3140A>G",
"hgvs_p": "p.His1047Arg",
"transcript": "ENST00000876545.1",
"protein_id": "ENSP00000546604.1",
"transcript_support_level": null,
"aa_start": 1047,
"aa_end": null,
"aa_length": 1068,
"cds_start": 3140,
"cds_end": null,
"cds_length": 3207,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876545.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.3140A>G",
"hgvs_p": "p.His1047Arg",
"transcript": "ENST00000913499.1",
"protein_id": "ENSP00000583558.1",
"transcript_support_level": null,
"aa_start": 1047,
"aa_end": null,
"aa_length": 1068,
"cds_start": 3140,
"cds_end": null,
"cds_length": 3207,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913499.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.3140A>G",
"hgvs_p": "p.His1047Arg",
"transcript": "ENST00000913500.1",
"protein_id": "ENSP00000583559.1",
"transcript_support_level": null,
"aa_start": 1047,
"aa_end": null,
"aa_length": 1068,
"cds_start": 3140,
"cds_end": null,
"cds_length": 3207,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913500.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.3140A>G",
"hgvs_p": "p.His1047Arg",
"transcript": "ENST00000955189.1",
"protein_id": "ENSP00000625248.1",
"transcript_support_level": null,
"aa_start": 1047,
"aa_end": null,
"aa_length": 1068,
"cds_start": 3140,
"cds_end": null,
"cds_length": 3207,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955189.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.3140A>G",
"hgvs_p": "p.His1047Arg",
"transcript": "XM_006713658.5",
"protein_id": "XP_006713721.1",
"transcript_support_level": null,
"aa_start": 1047,
"aa_end": null,
"aa_length": 1068,
"cds_start": 3140,
"cds_end": null,
"cds_length": 3207,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006713658.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "c.*220A>G",
"hgvs_p": null,
"transcript": "ENST00000643187.1",
"protein_id": "ENSP00000493507.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1000,
"cds_start": null,
"cds_end": null,
"cds_length": 3003,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000643187.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "n.2163A>G",
"hgvs_p": null,
"transcript": "ENST00000462255.2",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000462255.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "n.4048A>G",
"hgvs_p": null,
"transcript": "ENST00000674534.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000674534.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "n.*1378A>G",
"hgvs_p": null,
"transcript": "ENST00000674622.1",
"protein_id": "ENSP00000502417.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000674622.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "n.5947A>G",
"hgvs_p": null,
"transcript": "ENST00000675467.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000675467.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "n.*1707A>G",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000675786.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "n.3035A>G",
"hgvs_p": null,
"transcript": "ENST00000675796.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000675796.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "n.*1378A>G",
"hgvs_p": null,
"transcript": "ENST00000674622.1",
"protein_id": "ENSP00000502417.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000674622.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"hgvs_c": "n.*1707A>G",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000675786.1"
}
],
"gene_symbol": "PIK3CA",
"gene_hgnc_id": 8975,
"dbsnp": "rs121913279",
"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": 0.7534078359603882,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.455,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5381,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.25,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.845,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1_Supporting,PS4,PS2_Moderate,PP2,PM2_Supporting,PS3_Moderate",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM1_Supporting",
"PS4",
"PS2_Moderate",
"PP2",
"PM2_Supporting",
"PS3_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_006218.4",
"gene_symbol": "PIK3CA",
"hgnc_id": 8975,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3140A>G",
"hgvs_p": "p.His1047Arg"
}
],
"clinvar_disease": " EPITHELIAL, SOMATIC,Abnormal cardiovascular system morphology,Breast adenocarcinoma,Breast carcinoma,CEREBRAL CAVERNOUS MALFORMATIONS 4,CLAPO syndrome,CLOVES syndrome,Carcinoma of colon,Cerebrofacial Vascular Metameric Syndrome (CVMS),Congenital macrodactylia,Gastric cancer,Hepatocellular carcinoma,Klippel-Trenaunay-like-Syndrome,Lip and oral cavity carcinoma,MACRODACTYLY,Megalencephaly-capillary malformation-polymicrogyria syndrome,Neoplasm,Non-small cell lung carcinoma,OVARIAN CANCER,Ovarian neoplasm,Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes,PIK3CA related overgrowth syndrome,PIK3CA-Related Overgrowth Spectrum Disorders,PIK3CA-related disorder,Rare combined vascular malformation,Rare venous malformation,Rosette-forming glioneuronal tumor,Seborrheic keratosis,Segmental undergrowth associated with lymphatic malformation,Segmental undergrowth associated with mainly venous malformation with capillary component,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:18 LP:1 US:1 O:1",
"phenotype_combined": "Carcinoma of colon|Hepatocellular carcinoma|Non-small cell lung carcinoma|Seborrheic keratosis|Breast adenocarcinoma|OVARIAN CANCER, EPITHELIAL, SOMATIC|CLOVES syndrome|Ovarian neoplasm|PIK3CA related overgrowth syndrome|Neoplasm|Rosette-forming glioneuronal tumor|MACRODACTYLY, SOMATIC|not provided|Lip and oral cavity carcinoma|Abnormal cardiovascular system morphology|CEREBRAL CAVERNOUS MALFORMATIONS 4, SOMATIC|CLAPO syndrome|Cerebrofacial Vascular Metameric Syndrome (CVMS)|Segmental undergrowth associated with mainly venous malformation with capillary component|Segmental undergrowth associated with lymphatic malformation|Megalencephaly-capillary malformation-polymicrogyria syndrome|Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes|Congenital macrodactylia|Gastric cancer|Breast carcinoma|Klippel-Trenaunay-like-Syndrome|Rare venous malformation|Rare combined vascular malformation|PIK3CA-related disorder|PIK3CA-Related Overgrowth Spectrum Disorders",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}