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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: 3-179209622-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=179209622&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BA1",
"PM1_Supporting",
"BS2",
"PP2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PIK3CA",
"hgnc_id": 8975,
"hgvs_c": "c.1173A>G",
"hgvs_p": "p.Ile391Met",
"inheritance_mode": "AD,Unknown",
"pathogenic_score": 2,
"score": -10,
"transcript": "NM_006218.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BA1,PM1_Supporting,BS2,PP2",
"acmg_score": -10,
"allele_count_reference_population": 106360,
"alphamissense_prediction": null,
"alphamissense_score": 0.0808,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"chr": "3",
"clinvar_classification": "Benign",
"clinvar_disease": "Cowden syndrome,Cowden syndrome 5,Neoplasm,Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes,not provided,not specified",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "US:1 B:6 O:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0018924474716186523,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "I",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9259,
"cdna_start": 1496,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1173,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_006218.4",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1173A>G",
"hgvs_p": "p.Ile391Met",
"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": "M",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "I",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9259,
"cdna_start": 1496,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1173,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000263967.4",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1173A>G",
"hgvs_p": "p.Ile391Met",
"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": "M",
"aa_end": null,
"aa_length": 1078,
"aa_ref": "I",
"aa_start": 401,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4417,
"cdna_start": 1627,
"cds_end": null,
"cds_length": 3237,
"cds_start": 1203,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000955190.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1203A>G",
"hgvs_p": "p.Ile401Met",
"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": "M",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "I",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4204,
"cdna_start": 1397,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1173,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000876545.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1173A>G",
"hgvs_p": "p.Ile391Met",
"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": "M",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "I",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6910,
"cdna_start": 1747,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1173,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000913499.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1173A>G",
"hgvs_p": "p.Ile391Met",
"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": "M",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "I",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5533,
"cdna_start": 2538,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1173,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000913500.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1173A>G",
"hgvs_p": "p.Ile391Met",
"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": "M",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "I",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4545,
"cdna_start": 1754,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1173,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000955189.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1173A>G",
"hgvs_p": "p.Ile391Met",
"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": "M",
"aa_end": null,
"aa_length": 1000,
"aa_ref": "I",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4130,
"cdna_start": 1279,
"cds_end": null,
"cds_length": 3003,
"cds_start": 1173,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000643187.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1173A>G",
"hgvs_p": "p.Ile391Met",
"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": "M",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "I",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9106,
"cdna_start": 1343,
"cds_end": null,
"cds_length": 3207,
"cds_start": 1173,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_006713658.5",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "c.1173A>G",
"hgvs_p": "p.Ile391Met",
"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": 4835,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000674534.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.927A>G",
"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": "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": 6,
"exon_rank_end": null,
"feature": "ENST00000675467.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.3980A>G",
"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": 7,
"exon_rank_end": null,
"feature": "ENST00000675786.1",
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"hgvs_c": "n.1173A>G",
"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": "rs2230461",
"effect": "missense_variant",
"frequency_reference_population": 0.0660819,
"gene_hgnc_id": 8975,
"gene_symbol": "PIK3CA",
"gnomad_exomes_ac": 91077,
"gnomad_exomes_af": 0.062492,
"gnomad_exomes_homalt": 3729,
"gnomad_genomes_ac": 15283,
"gnomad_genomes_af": 0.10048,
"gnomad_genomes_homalt": 1192,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 4921,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|not provided|Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes|Neoplasm|Cowden syndrome|Cowden syndrome 5",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.333,
"pos": 179209622,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.236,
"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"
}
]
}