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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: 3-64099129-GGG-CGC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=64099129&ref=GGG&alt=CGC&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "PRICKLE2",
"hgnc_id": 20340,
"hgvs_c": "c.2455_2457delCCCinsGCG",
"hgvs_p": "p.Pro819Ala",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_198859.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "PRICKLE2-AS1",
"hgnc_id": null,
"hgvs_c": "n.2503_2505delGGGinsCGC",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": 0,
"transcript": "ENST00000482609.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_score": 0,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "CGC",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 844,
"aa_ref": "P",
"aa_start": 819,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9947,
"cdna_start": 3054,
"cds_end": null,
"cds_length": 2535,
"cds_start": 2455,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_198859.4",
"gene_hgnc_id": 20340,
"gene_symbol": "PRICKLE2",
"hgvs_c": "c.2455_2457delCCCinsGCG",
"hgvs_p": "p.Pro819Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000638394.2",
"protein_coding": true,
"protein_id": "NP_942559.1",
"strand": false,
"transcript": "NM_198859.4",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 844,
"aa_ref": "P",
"aa_start": 819,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9947,
"cdna_start": 3054,
"cds_end": null,
"cds_length": 2535,
"cds_start": 2455,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000638394.2",
"gene_hgnc_id": 20340,
"gene_symbol": "PRICKLE2",
"hgvs_c": "c.2455_2457delCCCinsGCG",
"hgvs_p": "p.Pro819Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_198859.4",
"protein_coding": true,
"protein_id": "ENSP00000492363.1",
"strand": false,
"transcript": "ENST00000638394.2",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 6505,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000482609.1",
"gene_hgnc_id": null,
"gene_symbol": "PRICKLE2-AS1",
"hgvs_c": "n.2503_2505delGGGinsCGC",
"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": "ENST00000482609.1",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 900,
"aa_ref": "P",
"aa_start": 875,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7918,
"cdna_start": 2660,
"cds_end": null,
"cds_length": 2703,
"cds_start": 2623,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000295902.11",
"gene_hgnc_id": 20340,
"gene_symbol": "PRICKLE2",
"hgvs_c": "c.2623_2625delCCCinsGCG",
"hgvs_p": "p.Pro875Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000295902.7",
"strand": false,
"transcript": "ENST00000295902.11",
"transcript_support_level": 5
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 874,
"aa_ref": "P",
"aa_start": 849,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3193,
"cdna_start": 2857,
"cds_end": null,
"cds_length": 2625,
"cds_start": 2545,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000906078.1",
"gene_hgnc_id": 20340,
"gene_symbol": "PRICKLE2",
"hgvs_c": "c.2545_2547delCCCinsGCG",
"hgvs_p": "p.Pro849Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576137.1",
"strand": false,
"transcript": "ENST00000906078.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 844,
"aa_ref": "P",
"aa_start": 819,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9665,
"cdna_start": 2772,
"cds_end": null,
"cds_length": 2535,
"cds_start": 2455,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001370528.1",
"gene_hgnc_id": 20340,
"gene_symbol": "PRICKLE2",
"hgvs_c": "c.2455_2457delCCCinsGCG",
"hgvs_p": "p.Pro819Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001357457.1",
"strand": false,
"transcript": "NM_001370528.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 844,
"aa_ref": "P",
"aa_start": 819,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8032,
"cdna_start": 2773,
"cds_end": null,
"cds_length": 2535,
"cds_start": 2455,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000564377.6",
"gene_hgnc_id": 20340,
"gene_symbol": "PRICKLE2",
"hgvs_c": "c.2455_2457delCCCinsGCG",
"hgvs_p": "p.Pro819Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000455004.2",
"strand": false,
"transcript": "ENST00000564377.6",
"transcript_support_level": 5
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 844,
"aa_ref": "P",
"aa_start": 819,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3548,
"cdna_start": 2923,
"cds_end": null,
"cds_length": 2535,
"cds_start": 2455,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000970252.1",
"gene_hgnc_id": 20340,
"gene_symbol": "PRICKLE2",
"hgvs_c": "c.2455_2457delCCCinsGCG",
"hgvs_p": "p.Pro819Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000640311.1",
"strand": false,
"transcript": "ENST00000970252.1",
"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": 4446,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000638436.1",
"gene_hgnc_id": 20340,
"gene_symbol": "PRICKLE2",
"hgvs_c": "n.1056_1058delCCCinsGCG",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000638436.1",
"transcript_support_level": 6
},
{
"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": 3704,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000640303.1",
"gene_hgnc_id": 20340,
"gene_symbol": "PRICKLE2",
"hgvs_c": "n.3094_3096delCCCinsGCG",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000640303.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 6505,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NR_045697.1",
"gene_hgnc_id": 40916,
"gene_symbol": "PRICKLE2-AS1",
"hgvs_c": "n.2503_2505delGGGinsCGC",
"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": "NR_045697.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 664,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000476308.2",
"gene_hgnc_id": null,
"gene_symbol": "PRICKLE2-AS1",
"hgvs_c": "n.-105_-103delGGGinsCGC",
"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": "ENST00000476308.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 404,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000835896.1",
"gene_hgnc_id": null,
"gene_symbol": "PRICKLE2-AS1",
"hgvs_c": "n.-105_-103delGGGinsCGC",
"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": "ENST00000835896.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 20340,
"gene_symbol": "PRICKLE2",
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.971,
"pos": 64099129,
"ref": "GGG",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_198859.4"
}
]
}