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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: 3-179198827-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=179198827&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 179198827,
"ref": "T",
"alt": "C",
"effect": "start_lost",
"transcript": "NM_006218.4",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"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.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_006218.4",
"protein_id": "NP_006209.2",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1068,
"cds_start": 2,
"cds_end": null,
"cds_length": 3207,
"cdna_start": 325,
"cdna_end": null,
"cdna_length": 9259,
"mane_select": "ENST00000263967.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"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.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000263967.4",
"protein_id": "ENSP00000263967.3",
"transcript_support_level": 2,
"aa_start": 1,
"aa_end": null,
"aa_length": 1068,
"cds_start": 2,
"cds_end": null,
"cds_length": 3207,
"cdna_start": 325,
"cdna_end": null,
"cdna_length": 9259,
"mane_select": "NM_006218.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"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.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000643187.1",
"protein_id": "ENSP00000493507.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1000,
"cds_start": 2,
"cds_end": null,
"cds_length": 3003,
"cdna_start": 108,
"cdna_end": null,
"cdna_length": 4130,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"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.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000468036.1",
"protein_id": "ENSP00000417479.1",
"transcript_support_level": 3,
"aa_start": 1,
"aa_end": null,
"aa_length": 117,
"cds_start": 2,
"cds_end": null,
"cds_length": 354,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 620,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"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.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000477735.1",
"protein_id": "ENSP00000418145.1",
"transcript_support_level": 4,
"aa_start": 1,
"aa_end": null,
"aa_length": 20,
"cds_start": 2,
"cds_end": null,
"cds_length": 63,
"cdna_start": 184,
"cdna_end": null,
"cdna_length": 245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"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.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "XM_006713658.5",
"protein_id": "XP_006713721.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1068,
"cds_start": 2,
"cds_end": null,
"cds_length": 3207,
"cdna_start": 172,
"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.2809T>C",
"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.2T>C",
"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": "rs2108384932",
"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": 0.9834909439086914,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.808,
"revel_prediction": "Pathogenic",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.31,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.622,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.03,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PM2",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PVS1_Moderate",
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006218.4",
"gene_symbol": "PIK3CA",
"hgnc_id": 8975,
"effects": [
"start_lost"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?"
}
],
"clinvar_disease": "Cowden syndrome 5",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Cowden syndrome 5",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}