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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: 1-233025234-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=233025234&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 233025234,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_014801.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.4517T>C",
"hgvs_p": "p.Leu1506Pro",
"transcript": "NM_014801.4",
"protein_id": "NP_055616.3",
"transcript_support_level": null,
"aa_start": 1506,
"aa_end": null,
"aa_length": 2137,
"cds_start": 4517,
"cds_end": null,
"cds_length": 6414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000258229.14",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014801.4"
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.4517T>C",
"hgvs_p": "p.Leu1506Pro",
"transcript": "ENST00000258229.14",
"protein_id": "ENSP00000258229.8",
"transcript_support_level": 5,
"aa_start": 1506,
"aa_end": null,
"aa_length": 2137,
"cds_start": 4517,
"cds_end": null,
"cds_length": 6414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014801.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000258229.14"
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.4142T>C",
"hgvs_p": "p.Leu1381Pro",
"transcript": "ENST00000912675.1",
"protein_id": "ENSP00000582734.1",
"transcript_support_level": null,
"aa_start": 1381,
"aa_end": null,
"aa_length": 2012,
"cds_start": 4142,
"cds_end": null,
"cds_length": 6039,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912675.1"
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.473T>C",
"hgvs_p": "p.Leu158Pro",
"transcript": "ENST00000344698.6",
"protein_id": "ENSP00000340759.2",
"transcript_support_level": 2,
"aa_start": 158,
"aa_end": null,
"aa_length": 777,
"cds_start": 473,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000344698.6"
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.4268T>C",
"hgvs_p": "p.Leu1423Pro",
"transcript": "XM_047430870.1",
"protein_id": "XP_047286826.1",
"transcript_support_level": null,
"aa_start": 1423,
"aa_end": null,
"aa_length": 2054,
"cds_start": 4268,
"cds_end": null,
"cds_length": 6165,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047430870.1"
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.3908T>C",
"hgvs_p": "p.Leu1303Pro",
"transcript": "XM_047430871.1",
"protein_id": "XP_047286827.1",
"transcript_support_level": null,
"aa_start": 1303,
"aa_end": null,
"aa_length": 1934,
"cds_start": 3908,
"cds_end": null,
"cds_length": 5805,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047430871.1"
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.2291T>C",
"hgvs_p": "p.Leu764Pro",
"transcript": "XM_011544278.3",
"protein_id": "XP_011542580.2",
"transcript_support_level": null,
"aa_start": 764,
"aa_end": null,
"aa_length": 1395,
"cds_start": 2291,
"cds_end": null,
"cds_length": 4188,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011544278.3"
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.1649T>C",
"hgvs_p": "p.Leu550Pro",
"transcript": "XM_047430873.1",
"protein_id": "XP_047286829.1",
"transcript_support_level": null,
"aa_start": 550,
"aa_end": null,
"aa_length": 1181,
"cds_start": 1649,
"cds_end": null,
"cds_length": 3546,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047430873.1"
},
{
"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": 26,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.4352-8080T>C",
"hgvs_p": null,
"transcript": "XM_047430872.1",
"protein_id": "XP_047286828.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1468,
"cds_start": null,
"cds_end": null,
"cds_length": 4407,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047430872.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "n.399T>C",
"hgvs_p": null,
"transcript": "ENST00000522067.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "retained_intron",
"feature": "ENST00000522067.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "n.1415-8080T>C",
"hgvs_p": null,
"transcript": "ENST00000462233.5",
"protein_id": "ENSP00000428488.1",
"transcript_support_level": 2,
"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": "nonsense_mediated_decay",
"feature": "ENST00000462233.5"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "n.*29T>C",
"hgvs_p": null,
"transcript": "ENST00000429988.2",
"protein_id": null,
"transcript_support_level": 4,
"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": "retained_intron",
"feature": "ENST00000429988.2"
}
],
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"dbsnp": "rs1481629638",
"frequency_reference_population": 6.841312e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84131e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8876345157623291,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.77,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9609,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.939,
"phylop100way_prediction": "Pathogenic",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_014801.4",
"gene_symbol": "PCNX2",
"hgnc_id": 8736,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4517T>C",
"hgvs_p": "p.Leu1506Pro"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}