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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: 3-64175286-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=64175286&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 64175286,
"ref": "T",
"alt": "A",
"effect": "intron_variant",
"transcript": "NM_198859.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PRICKLE2",
"gene_hgnc_id": 20340,
"hgvs_c": "c.145-12157A>T",
"hgvs_p": null,
"transcript": "NM_198859.4",
"protein_id": "NP_942559.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 844,
"cds_start": null,
"cds_end": null,
"cds_length": 2535,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9947,
"mane_select": "ENST00000638394.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_198859.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PRICKLE2",
"gene_hgnc_id": 20340,
"hgvs_c": "c.145-12157A>T",
"hgvs_p": null,
"transcript": "ENST00000638394.2",
"protein_id": "ENSP00000492363.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 844,
"cds_start": null,
"cds_end": null,
"cds_length": 2535,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9947,
"mane_select": "NM_198859.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000638394.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PRICKLE2",
"gene_hgnc_id": 20340,
"hgvs_c": "c.313-12157A>T",
"hgvs_p": null,
"transcript": "ENST00000295902.11",
"protein_id": "ENSP00000295902.7",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 900,
"cds_start": null,
"cds_end": null,
"cds_length": 2703,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7918,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295902.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PRICKLE2",
"gene_hgnc_id": 20340,
"hgvs_c": "c.145-12157A>T",
"hgvs_p": null,
"transcript": "ENST00000906078.1",
"protein_id": "ENSP00000576137.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 874,
"cds_start": null,
"cds_end": null,
"cds_length": 2625,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3193,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906078.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PRICKLE2",
"gene_hgnc_id": 20340,
"hgvs_c": "c.145-12157A>T",
"hgvs_p": null,
"transcript": "NM_001370528.1",
"protein_id": "NP_001357457.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 844,
"cds_start": null,
"cds_end": null,
"cds_length": 2535,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9665,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001370528.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PRICKLE2",
"gene_hgnc_id": 20340,
"hgvs_c": "c.145-12157A>T",
"hgvs_p": null,
"transcript": "ENST00000564377.6",
"protein_id": "ENSP00000455004.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 844,
"cds_start": null,
"cds_end": null,
"cds_length": 2535,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8032,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000564377.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PRICKLE2",
"gene_hgnc_id": 20340,
"hgvs_c": "c.145-12157A>T",
"hgvs_p": null,
"transcript": "ENST00000970252.1",
"protein_id": "ENSP00000640311.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 844,
"cds_start": null,
"cds_end": null,
"cds_length": 2535,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3548,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970252.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PRICKLE2",
"gene_hgnc_id": 20340,
"hgvs_c": "c.292-12157A>T",
"hgvs_p": null,
"transcript": "ENST00000498162.2",
"protein_id": "ENSP00000419951.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 141,
"cds_start": null,
"cds_end": null,
"cds_length": 426,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 428,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000498162.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": null,
"strand": true,
"consequences": [
"intragenic_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": null,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX3P4",
"gene_hgnc_id": 44643,
"hgvs_c": "n.64175286T>A",
"hgvs_p": null,
"transcript": null,
"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": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX3P4",
"gene_hgnc_id": 44643,
"hgvs_c": "n.*139T>A",
"hgvs_p": null,
"transcript": "ENST00000470828.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 747,
"mane_select": null,
"mane_plus": null,
"biotype": "processed_pseudogene",
"feature": "ENST00000470828.1"
}
],
"gene_symbol": "PRICKLE2",
"gene_hgnc_id": 20340,
"dbsnp": "rs149105",
"frequency_reference_population": 0.42478645,
"hom_count_reference_population": 14373,
"allele_count_reference_population": 64949,
"gnomad_exomes_af": 0.383673,
"gnomad_genomes_af": 0.425052,
"gnomad_exomes_ac": 376,
"gnomad_genomes_ac": 64573,
"gnomad_exomes_homalt": 65,
"gnomad_genomes_homalt": 14308,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9399999976158142,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.94,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.099,
"phylop100way_prediction": "Benign",
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_198859.4",
"gene_symbol": "PRICKLE2",
"hgnc_id": 20340,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.145-12157A>T",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "",
"gene_symbol": "PRDX3P4",
"hgnc_id": 44643,
"effects": [
"intragenic_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.64175286T>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}