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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: 1-232984475-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=232984475&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 232984475,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "NM_014801.4",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.6243C>T",
"hgvs_p": "p.His2081His",
"transcript": "NM_014801.4",
"protein_id": "NP_055616.3",
"transcript_support_level": null,
"aa_start": 2081,
"aa_end": null,
"aa_length": 2137,
"cds_start": 6243,
"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": "H",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.6243C>T",
"hgvs_p": "p.His2081His",
"transcript": "ENST00000258229.14",
"protein_id": "ENSP00000258229.8",
"transcript_support_level": 5,
"aa_start": 2081,
"aa_end": null,
"aa_length": 2137,
"cds_start": 6243,
"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": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.5868C>T",
"hgvs_p": "p.His1956His",
"transcript": "ENST00000912675.1",
"protein_id": "ENSP00000582734.1",
"transcript_support_level": null,
"aa_start": 1956,
"aa_end": null,
"aa_length": 2012,
"cds_start": 5868,
"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": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.5994C>T",
"hgvs_p": "p.His1998His",
"transcript": "XM_047430870.1",
"protein_id": "XP_047286826.1",
"transcript_support_level": null,
"aa_start": 1998,
"aa_end": null,
"aa_length": 2054,
"cds_start": 5994,
"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": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.5634C>T",
"hgvs_p": "p.His1878His",
"transcript": "XM_047430871.1",
"protein_id": "XP_047286827.1",
"transcript_support_level": null,
"aa_start": 1878,
"aa_end": null,
"aa_length": 1934,
"cds_start": 5634,
"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": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.4017C>T",
"hgvs_p": "p.His1339His",
"transcript": "XM_011544278.3",
"protein_id": "XP_011542580.2",
"transcript_support_level": null,
"aa_start": 1339,
"aa_end": null,
"aa_length": 1395,
"cds_start": 4017,
"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": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.3375C>T",
"hgvs_p": "p.His1125His",
"transcript": "XM_047430873.1",
"protein_id": "XP_047286829.1",
"transcript_support_level": null,
"aa_start": 1125,
"aa_end": null,
"aa_length": 1181,
"cds_start": 3375,
"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": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.*1479C>T",
"hgvs_p": null,
"transcript": "ENST00000344698.6",
"protein_id": "ENSP00000340759.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 777,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "n.*1582C>T",
"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": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "n.45C>T",
"hgvs_p": null,
"transcript": "ENST00000462762.1",
"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": "pseudogene",
"feature": "ENST00000462762.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "n.258C>T",
"hgvs_p": null,
"transcript": "ENST00000496675.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000496675.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "n.*1582C>T",
"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"
}
],
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"dbsnp": "rs61741049",
"frequency_reference_population": 0.0019107624,
"hom_count_reference_population": 37,
"allele_count_reference_population": 3080,
"gnomad_exomes_af": 0.00115916,
"gnomad_genomes_af": 0.00911718,
"gnomad_exomes_ac": 1692,
"gnomad_genomes_ac": 1388,
"gnomad_exomes_homalt": 18,
"gnomad_genomes_homalt": 19,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8199999928474426,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.82,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.551,
"phylop100way_prediction": "Benign",
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_014801.4",
"gene_symbol": "PCNX2",
"hgnc_id": 8736,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.6243C>T",
"hgvs_p": "p.His2081His"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}