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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: 1-233227227-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=233227227&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"stop_gained",
"splice_region_variant"
],
"gene_symbol": "PCNX2",
"hgnc_id": 8736,
"hgvs_c": "c.2503C>T",
"hgvs_p": "p.Arg835*",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_014801.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.6,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6000000238418579,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2137,
"aa_ref": "R",
"aa_start": 835,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7530,
"cdna_start": 2750,
"cds_end": null,
"cds_length": 6414,
"cds_start": 2503,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 34,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_014801.4",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "c.2503C>T",
"hgvs_p": "p.Arg835*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000258229.14",
"protein_coding": true,
"protein_id": "NP_055616.3",
"strand": false,
"transcript": "NM_014801.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2137,
"aa_ref": "R",
"aa_start": 835,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7530,
"cdna_start": 2750,
"cds_end": null,
"cds_length": 6414,
"cds_start": 2503,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 34,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000258229.14",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "c.2503C>T",
"hgvs_p": "p.Arg835*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014801.4",
"protein_coding": true,
"protein_id": "ENSP00000258229.8",
"strand": false,
"transcript": "ENST00000258229.14",
"transcript_support_level": 5
},
{
"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": 2183,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000475463.6",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "n.649-9043C>T",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000429360.1",
"strand": false,
"transcript": "ENST00000475463.6",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2012,
"aa_ref": "R",
"aa_start": 835,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7157,
"cdna_start": 2754,
"cds_end": null,
"cds_length": 6039,
"cds_start": 2503,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 31,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000912675.1",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "c.2503C>T",
"hgvs_p": "p.Arg835*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582734.1",
"strand": false,
"transcript": "ENST00000912675.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 180,
"aa_ref": "R",
"aa_start": 15,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 545,
"cdna_start": 43,
"cds_end": null,
"cds_length": 545,
"cds_start": 43,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000518351.2",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "c.43C>T",
"hgvs_p": "p.Arg15*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000429231.1",
"strand": false,
"transcript": "ENST00000518351.2",
"transcript_support_level": 4
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2054,
"aa_ref": "R",
"aa_start": 752,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7231,
"cdna_start": 2451,
"cds_end": null,
"cds_length": 6165,
"cds_start": 2254,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 34,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047430870.1",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "c.2254C>T",
"hgvs_p": "p.Arg752*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047286826.1",
"strand": false,
"transcript": "XM_047430870.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1934,
"aa_ref": "R",
"aa_start": 632,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6909,
"cdna_start": 2129,
"cds_end": null,
"cds_length": 5805,
"cds_start": 1894,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 32,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047430871.1",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "c.1894C>T",
"hgvs_p": "p.Arg632*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047286827.1",
"strand": false,
"transcript": "XM_047430871.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1468,
"aa_ref": "R",
"aa_start": 835,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4754,
"cdna_start": 2750,
"cds_end": null,
"cds_length": 4407,
"cds_start": 2503,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 26,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047430872.1",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "c.2503C>T",
"hgvs_p": "p.Arg835*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047286828.1",
"strand": false,
"transcript": "XM_047430872.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1395,
"aa_ref": "R",
"aa_start": 93,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5129,
"cdna_start": 349,
"cds_end": null,
"cds_length": 4188,
"cds_start": 277,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 27,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_011544278.3",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "c.277C>T",
"hgvs_p": "p.Arg93*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011542580.2",
"strand": false,
"transcript": "XM_011544278.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1364,
"aa_ref": "R",
"aa_start": 835,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4533,
"cdna_start": 2750,
"cds_end": null,
"cds_length": 4095,
"cds_start": 2503,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 24,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_006711816.4",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "c.2503C>T",
"hgvs_p": "p.Arg835*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006711879.1",
"strand": false,
"transcript": "XM_006711816.4",
"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": 1828,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000324142.4",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "n.709C>T",
"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": "ENST00000324142.4",
"transcript_support_level": 2
},
{
"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": 439,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000519530.1",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "n.121C>T",
"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": "ENST00000519530.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4462,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XR_001737430.2",
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"hgvs_c": "n.2750C>T",
"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": "XR_001737430.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.0351850416911894,
"dbsnp": "rs74147307",
"effect": "stop_gained,splice_region_variant",
"frequency_reference_population": 0.0000043443993,
"gene_hgnc_id": 8736,
"gene_symbol": "PCNX2",
"gnomad_exomes_ac": 6,
"gnomad_exomes_af": 0.00000411232,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000656858,
"gnomad_genomes_homalt": 0,
"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": 1.137,
"pos": 233227227,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.3400000035762787,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Uncertain_significance",
"spliceai_max_score": 0.21,
"transcript": "NM_014801.4"
}
]
}