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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: 3-179230077-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=179230077&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1_Supporting",
"PS4",
"PS2",
"PP2",
"PM2_Supporting"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PIK3CA",
"hgnc_id": 8975,
"hgvs_c": "c.2740G>A",
"hgvs_p": "p.Gly914Arg",
"inheritance_mode": "AD,Unknown",
"pathogenic_score": 11,
"score": 11,
"transcript": "NM_006218.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1_Supporting,PS4,PS2,PP2,PM2_Supporting",
"acmg_score": 11,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9956,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.38,
"chr": "3",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Abnormal cardiovascular system morphology,Abnormal cerebral morphology,Angioosteohypertrophic syndrome,CLOVES syndrome,Cowden syndrome,Cowden syndrome 5,Inborn genetic diseases,Megalencephaly-capillary malformation-polymicrogyria syndrome,Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes,PIK3C1-related disorder,PIK3CA related overgrowth syndrome,PIK3CA-related disorder,not provided",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:13 LP:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9727920293807983,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "G",
"aa_start": 914,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9259,
"cdna_start": 3063,
"cds_end": null,
"cds_length": 3207,
"cds_start": 2740,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_006218.4",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.2740G>A",
"hgvs_p": "p.Gly914Arg",
"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": "R",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "G",
"aa_start": 914,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9259,
"cdna_start": 3063,
"cds_end": null,
"cds_length": 3207,
"cds_start": 2740,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000263967.4",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.2740G>A",
"hgvs_p": "p.Gly914Arg",
"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": "R",
"aa_end": null,
"aa_length": 1078,
"aa_ref": "G",
"aa_start": 924,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4417,
"cdna_start": 3194,
"cds_end": null,
"cds_length": 3237,
"cds_start": 2770,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000955190.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.2770G>A",
"hgvs_p": "p.Gly924Arg",
"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": "R",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "G",
"aa_start": 914,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4204,
"cdna_start": 2964,
"cds_end": null,
"cds_length": 3207,
"cds_start": 2740,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000876545.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.2740G>A",
"hgvs_p": "p.Gly914Arg",
"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": "R",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "G",
"aa_start": 914,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6910,
"cdna_start": 3314,
"cds_end": null,
"cds_length": 3207,
"cds_start": 2740,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000913499.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.2740G>A",
"hgvs_p": "p.Gly914Arg",
"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": "R",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "G",
"aa_start": 914,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5533,
"cdna_start": 4105,
"cds_end": null,
"cds_length": 3207,
"cds_start": 2740,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000913500.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.2740G>A",
"hgvs_p": "p.Gly914Arg",
"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": "R",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "G",
"aa_start": 914,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4545,
"cdna_start": 3321,
"cds_end": null,
"cds_length": 3207,
"cds_start": 2740,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000955189.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.2740G>A",
"hgvs_p": "p.Gly914Arg",
"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": "R",
"aa_end": null,
"aa_length": 1000,
"aa_ref": "G",
"aa_start": 914,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4130,
"cdna_start": 2846,
"cds_end": null,
"cds_length": 3003,
"cds_start": 2740,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000643187.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.2740G>A",
"hgvs_p": "p.Gly914Arg",
"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": "R",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "G",
"aa_start": 914,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9106,
"cdna_start": 2910,
"cds_end": null,
"cds_length": 3207,
"cds_start": 2740,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_006713658.5",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.2740G>A",
"hgvs_p": "p.Gly914Arg",
"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": 9,
"exon_rank_end": null,
"feature": "ENST00000462255.2",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.1763G>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": 13,
"exon_rank_end": null,
"feature": "ENST00000674534.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.3648G>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": 10,
"exon_rank_end": null,
"feature": "ENST00000674622.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.*978G>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": 18,
"exon_rank_end": null,
"feature": "ENST00000675467.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.5547G>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": 19,
"exon_rank_end": null,
"feature": "ENST00000675786.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.*1307G>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": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3845,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000675796.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.2635G>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": "ENST00000675796.1",
"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": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000674622.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.*978G>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": "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": 19,
"exon_rank_end": null,
"feature": "ENST00000675786.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.*1307G>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": "rs587776932",
"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",
"phenotype_combined": "Megalencephaly-capillary malformation-polymicrogyria syndrome|not provided|Abnormal cardiovascular system morphology|Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes|PIK3CA related overgrowth syndrome|Cowden syndrome 5|CLOVES syndrome|PIK3CA-related disorder|Inborn genetic diseases|PIK3C1-related disorder|Cowden syndrome|Angioosteohypertrophic syndrome|Abnormal cerebral morphology",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.492,
"pos": 179230077,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.871,
"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"
}
]
}