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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: 5-141344220-GGA-CGC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=141344220&ref=GGA&alt=CGC&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "PCDHGA3",
"hgnc_id": 8701,
"hgvs_c": "c.187_189delGGAinsCGC",
"hgvs_p": "p.Gly63Arg",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_018916.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [],
"effects": [
"intron_variant"
],
"gene_symbol": "PCDHGA2",
"hgnc_id": 8700,
"hgvs_c": "c.2424+2825_2424+2827delGGAinsCGC",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_018915.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [],
"effects": [
"intron_variant"
],
"gene_symbol": "PCDHGA1",
"hgnc_id": 8696,
"hgvs_c": "c.2421+11115_2421+11117delGGAinsCGC",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_018912.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [],
"effects": [
"intragenic_variant"
],
"gene_symbol": "PCDHG@",
"hgnc_id": 8695,
"hgvs_c": "n.141344220_141344222delGGAinsCGC",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": 0,
"transcript": "",
"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": "5",
"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": "R",
"aa_end": null,
"aa_length": 932,
"aa_ref": "G",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4806,
"cdna_start": 392,
"cds_end": null,
"cds_length": 2799,
"cds_start": 187,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_018916.4",
"gene_hgnc_id": 8701,
"gene_symbol": "PCDHGA3",
"hgvs_c": "c.187_189delGGAinsCGC",
"hgvs_p": "p.Gly63Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000253812.8",
"protein_coding": true,
"protein_id": "NP_061739.2",
"strand": true,
"transcript": "NM_018916.4",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 932,
"aa_ref": "G",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4806,
"cdna_start": 392,
"cds_end": null,
"cds_length": 2799,
"cds_start": 187,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000253812.8",
"gene_hgnc_id": 8701,
"gene_symbol": "PCDHGA3",
"hgvs_c": "c.187_189delGGAinsCGC",
"hgvs_p": "p.Gly63Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018916.4",
"protein_coding": true,
"protein_id": "ENSP00000253812.7",
"strand": true,
"transcript": "ENST00000253812.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 932,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4813,
"cdna_start": null,
"cds_end": null,
"cds_length": 2799,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_018915.4",
"gene_hgnc_id": 8700,
"gene_symbol": "PCDHGA2",
"hgvs_c": "c.2424+2825_2424+2827delGGAinsCGC",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000394576.3",
"protein_coding": true,
"protein_id": "NP_061738.1",
"strand": true,
"transcript": "NM_018915.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 932,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4813,
"cdna_start": null,
"cds_end": null,
"cds_length": 2799,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000394576.3",
"gene_hgnc_id": 8700,
"gene_symbol": "PCDHGA2",
"hgvs_c": "c.2424+2825_2424+2827delGGAinsCGC",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018915.4",
"protein_coding": true,
"protein_id": "ENSP00000378077.2",
"strand": true,
"transcript": "ENST00000394576.3",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 931,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4769,
"cdna_start": null,
"cds_end": null,
"cds_length": 2796,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_018912.3",
"gene_hgnc_id": 8696,
"gene_symbol": "PCDHGA1",
"hgvs_c": "c.2421+11115_2421+11117delGGAinsCGC",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000517417.3",
"protein_coding": true,
"protein_id": "NP_061735.1",
"strand": true,
"transcript": "NM_018912.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 931,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4769,
"cdna_start": null,
"cds_end": null,
"cds_length": 2796,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000517417.3",
"gene_hgnc_id": 8696,
"gene_symbol": "PCDHGA1",
"hgvs_c": "c.2421+11115_2421+11117delGGAinsCGC",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018912.3",
"protein_coding": true,
"protein_id": "ENSP00000431083.1",
"strand": true,
"transcript": "ENST00000517417.3",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 829,
"aa_ref": "G",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3119,
"cdna_start": 392,
"cds_end": null,
"cds_length": 2490,
"cds_start": 187,
"consequences": [
"missense_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_032011.2",
"gene_hgnc_id": 8701,
"gene_symbol": "PCDHGA3",
"hgvs_c": "c.187_189delGGAinsCGC",
"hgvs_p": "p.Gly63Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_114400.1",
"strand": true,
"transcript": "NM_032011.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 829,
"aa_ref": "G",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2695,
"cdna_start": 392,
"cds_end": null,
"cds_length": 2490,
"cds_start": 187,
"consequences": [
"missense_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000619750.1",
"gene_hgnc_id": 8701,
"gene_symbol": "PCDHGA3",
"hgvs_c": "c.187_189delGGAinsCGC",
"hgvs_p": "p.Gly63Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000479265.1",
"strand": true,
"transcript": "ENST00000619750.1",
"transcript_support_level": 6
},
{
"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": 2712,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000612467.1",
"gene_hgnc_id": 8701,
"gene_symbol": "PCDHGA3",
"hgvs_c": "n.187_189delGGAinsCGC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000481801.1",
"strand": true,
"transcript": "ENST00000612467.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": null,
"canonical": null,
"cdna_end": null,
"cdna_length": null,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intragenic_variant"
],
"exon_count": null,
"exon_rank": null,
"exon_rank_end": null,
"feature": null,
"gene_hgnc_id": 8695,
"gene_symbol": "PCDHG@",
"hgvs_c": "n.141344220_141344222delGGAinsCGC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": null,
"protein_id": null,
"strand": true,
"transcript": null,
"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": 8701,
"gene_symbol": "PCDHGA3",
"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": "Benign",
"phylop100way_score": 0.608,
"pos": 141344220,
"ref": "GGA",
"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_018916.4"
}
]
}