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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: 3-179218303-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=179218303&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS1",
"PS3",
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PIK3CA",
"hgnc_id": 8975,
"hgvs_c": "c.1633G>A",
"hgvs_p": "p.Glu545Lys",
"inheritance_mode": "AD,Unknown",
"pathogenic_score": 25,
"score": 25,
"transcript": "NM_006218.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS1,PS3,PM1,PM2,PM5,PP2,PP3_Moderate,PP5_Very_Strong",
"acmg_score": 25,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9878,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.26,
"chr": "3",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": " EPITHELIAL, SOMATIC,Abnormal cardiovascular system morphology,Angioosteohypertrophic syndrome,Breast adenocarcinoma,CLOVES syndrome,Carcinoma of colon,Cerebrofacial Vascular Metameric Syndrome (CVMS),Eccrine angiomatous hamartoma,Gallbladder cancer,Gastric cancer,HEMIFACIAL MYOHYPERPLASIA,Megalencephaly-capillary malformation-polymicrogyria syndrome,Neoplasm,Non-small cell lung carcinoma,OVARIAN CANCER,Ovarian neoplasm,PIK3CA overgrowth syndrome,PIK3CA related overgrowth syndrome,Rare combined vascular malformation,Rare venous malformation,Sarcoma,Seborrheic keratosis,Segmental undergrowth associated with lymphatic malformation,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:8 LP:1 US:1 O:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8705136179924011,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "E",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9259,
"cdna_start": 1956,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1633,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_006218.4",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1633G>A",
"hgvs_p": "p.Glu545Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000263967.4",
"protein_coding": true,
"protein_id": "NP_006209.2",
"strand": true,
"transcript": "NM_006218.4",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "E",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9259,
"cdna_start": 1956,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1633,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000263967.4",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1633G>A",
"hgvs_p": "p.Glu545Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006218.4",
"protein_coding": true,
"protein_id": "ENSP00000263967.3",
"strand": true,
"transcript": "ENST00000263967.4",
"transcript_support_level": 2
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1078,
"aa_ref": "E",
"aa_start": 555,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4417,
"cdna_start": 2087,
"cds_end": null,
"cds_length": 3237,
"cds_start": 1663,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000955190.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1663G>A",
"hgvs_p": "p.Glu555Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625249.1",
"strand": true,
"transcript": "ENST00000955190.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "E",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4204,
"cdna_start": 1857,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1633,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000876545.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1633G>A",
"hgvs_p": "p.Glu545Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546604.1",
"strand": true,
"transcript": "ENST00000876545.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "E",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6910,
"cdna_start": 2207,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1633,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000913499.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1633G>A",
"hgvs_p": "p.Glu545Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000583558.1",
"strand": true,
"transcript": "ENST00000913499.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "E",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5533,
"cdna_start": 2998,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1633,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000913500.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1633G>A",
"hgvs_p": "p.Glu545Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000583559.1",
"strand": true,
"transcript": "ENST00000913500.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "E",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4545,
"cdna_start": 2214,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1633,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000955189.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1633G>A",
"hgvs_p": "p.Glu545Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625248.1",
"strand": true,
"transcript": "ENST00000955189.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1000,
"aa_ref": "E",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4130,
"cdna_start": 1739,
"cds_end": null,
"cds_length": 3003,
"cds_start": 1633,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000643187.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1633G>A",
"hgvs_p": "p.Glu545Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493507.1",
"strand": true,
"transcript": "ENST00000643187.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "E",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9106,
"cdna_start": 1803,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1633,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_006713658.5",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1633G>A",
"hgvs_p": "p.Glu545Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006713721.1",
"strand": true,
"transcript": "XM_006713658.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2882,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000462255.2",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.95G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000462255.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 4835,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 15,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000674534.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.1387G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000674534.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2348,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000674622.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.136G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000502417.1",
"strand": true,
"transcript": "ENST00000674622.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 7021,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000675467.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.4440G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000675467.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4148,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000675786.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.*200G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000502323.1",
"strand": true,
"transcript": "ENST00000675786.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4148,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000675786.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.*200G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000502323.1",
"strand": true,
"transcript": "ENST00000675786.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs104886003",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Carcinoma of colon|Seborrheic keratosis|Breast adenocarcinoma|OVARIAN CANCER, EPITHELIAL, SOMATIC|Non-small cell lung carcinoma|Megalencephaly-capillary malformation-polymicrogyria syndrome|Sarcoma|Ovarian neoplasm|not provided|CLOVES syndrome|Abnormal cardiovascular system morphology|PIK3CA related overgrowth syndrome|Cerebrofacial Vascular Metameric Syndrome (CVMS)|Segmental undergrowth associated with lymphatic malformation|Gallbladder cancer|Eccrine angiomatous hamartoma|Gastric cancer|HEMIFACIAL MYOHYPERPLASIA, SOMATIC|Angioosteohypertrophic syndrome|Rare venous malformation|Rare combined vascular malformation|Neoplasm|PIK3CA overgrowth syndrome",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.602,
"pos": 179218303,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.654,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006218.4"
}
]
}