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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: 5-141360566-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=141360566&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PCDHGB2",
"hgnc_id": 8709,
"hgvs_c": "c.431A>G",
"hgvs_p": "p.Glu144Gly",
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_018923.3",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PCDHGA4",
"hgnc_id": 8702,
"hgvs_c": "c.2514+2945A>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_018917.4",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PCDHGA2",
"hgnc_id": 8700,
"hgvs_c": "c.2424+19171A>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_018915.4",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PCDHGA3",
"hgnc_id": 8701,
"hgvs_c": "c.2424+14109A>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_018916.4",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PCDHGA1",
"hgnc_id": 8696,
"hgvs_c": "c.2421+27461A>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_018912.3",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PCDHGB1",
"hgnc_id": 8708,
"hgvs_c": "c.2409+7897A>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_018922.3",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"intragenic_variant"
],
"gene_symbol": "PCDHG@",
"hgnc_id": 8695,
"hgvs_c": "n.141360566A>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_score": 6,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.8004,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.36,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9667370319366455,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 931,
"aa_ref": "E",
"aa_start": 144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4740,
"cdna_start": 573,
"cds_end": null,
"cds_length": 2796,
"cds_start": 431,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_018923.3",
"gene_hgnc_id": 8709,
"gene_symbol": "PCDHGB2",
"hgvs_c": "c.431A>G",
"hgvs_p": "p.Glu144Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000522605.2",
"protein_coding": true,
"protein_id": "NP_061746.1",
"strand": true,
"transcript": "NM_018923.3",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 931,
"aa_ref": "E",
"aa_start": 144,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4740,
"cdna_start": 573,
"cds_end": null,
"cds_length": 2796,
"cds_start": 431,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000522605.2",
"gene_hgnc_id": 8709,
"gene_symbol": "PCDHGB2",
"hgvs_c": "c.431A>G",
"hgvs_p": "p.Glu144Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018923.3",
"protein_coding": true,
"protein_id": "ENSP00000429018.1",
"strand": true,
"transcript": "ENST00000522605.2",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 962,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4778,
"cdna_start": null,
"cds_end": null,
"cds_length": 2889,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_018917.4",
"gene_hgnc_id": 8702,
"gene_symbol": "PCDHGA4",
"hgvs_c": "c.2514+2945A>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000571252.3",
"protein_coding": true,
"protein_id": "NP_061740.2",
"strand": true,
"transcript": "NM_018917.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 962,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4778,
"cdna_start": null,
"cds_end": null,
"cds_length": 2889,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000571252.3",
"gene_hgnc_id": 8702,
"gene_symbol": "PCDHGA4",
"hgvs_c": "c.2514+2945A>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018917.4",
"protein_coding": true,
"protein_id": "ENSP00000458570.2",
"strand": true,
"transcript": "ENST00000571252.3",
"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+19171A>G",
"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": false,
"cdna_end": null,
"cdna_length": 4806,
"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_018916.4",
"gene_hgnc_id": 8701,
"gene_symbol": "PCDHGA3",
"hgvs_c": "c.2424+14109A>G",
"hgvs_p": null,
"intron_rank": 1,
"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": null,
"aa_end": null,
"aa_length": 932,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4806,
"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": "ENST00000253812.8",
"gene_hgnc_id": 8701,
"gene_symbol": "PCDHGA3",
"hgvs_c": "c.2424+14109A>G",
"hgvs_p": null,
"intron_rank": 1,
"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": 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+19171A>G",
"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+27461A>G",
"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+27461A>G",
"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": null,
"aa_end": null,
"aa_length": 927,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4748,
"cdna_start": null,
"cds_end": null,
"cds_length": 2784,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_018922.3",
"gene_hgnc_id": 8708,
"gene_symbol": "PCDHGB1",
"hgvs_c": "c.2409+7897A>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000523390.2",
"protein_coding": true,
"protein_id": "NP_061745.1",
"strand": true,
"transcript": "NM_018922.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 927,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4748,
"cdna_start": null,
"cds_end": null,
"cds_length": 2784,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000523390.2",
"gene_hgnc_id": 8708,
"gene_symbol": "PCDHGB1",
"hgvs_c": "c.2409+7897A>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018922.3",
"protein_coding": true,
"protein_id": "ENSP00000429273.1",
"strand": true,
"transcript": "ENST00000523390.2",
"transcript_support_level": 1
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 811,
"aa_ref": "E",
"aa_start": 144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2436,
"cdna_start": 431,
"cds_end": null,
"cds_length": 2436,
"cds_start": 431,
"consequences": [
"missense_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_032096.1",
"gene_hgnc_id": 8709,
"gene_symbol": "PCDHGB2",
"hgvs_c": "c.431A>G",
"hgvs_p": "p.Glu144Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_115267.1",
"strand": true,
"transcript": "NM_032096.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 811,
"aa_ref": "E",
"aa_start": 144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2588,
"cdna_start": 525,
"cds_end": null,
"cds_length": 2436,
"cds_start": 431,
"consequences": [
"missense_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000622527.1",
"gene_hgnc_id": 8709,
"gene_symbol": "PCDHGB2",
"hgvs_c": "c.431A>G",
"hgvs_p": "p.Glu144Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000481512.1",
"strand": true,
"transcript": "ENST00000622527.1",
"transcript_support_level": 6
},
{
"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.141360566A>G",
"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
},
{
"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": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000612467.1",
"gene_hgnc_id": 8701,
"gene_symbol": "PCDHGA3",
"hgvs_c": "n.*2003+14109A>G",
"hgvs_p": null,
"intron_rank": 2,
"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
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 8709,
"gene_symbol": "PCDHGB2",
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.208,
"pos": 141360566,
"ref": "A",
"revel_prediction": "Pathogenic",
"revel_score": 0.902,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_018923.3"
}
]
}