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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: 11-65634346-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=65634346&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 65634346,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_032223.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4691G>T",
"hgvs_p": "p.Arg1564Leu",
"transcript": "NM_032223.4",
"protein_id": "NP_115599.2",
"transcript_support_level": null,
"aa_start": 1564,
"aa_end": null,
"aa_length": 2034,
"cds_start": 4691,
"cds_end": null,
"cds_length": 6105,
"cdna_start": 5227,
"cdna_end": null,
"cdna_length": 7102,
"mane_select": "ENST00000355703.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032223.4"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4691G>T",
"hgvs_p": "p.Arg1564Leu",
"transcript": "ENST00000355703.4",
"protein_id": "ENSP00000347931.3",
"transcript_support_level": 5,
"aa_start": 1564,
"aa_end": null,
"aa_length": 2034,
"cds_start": 4691,
"cds_end": null,
"cds_length": 6105,
"cdna_start": 5227,
"cdna_end": null,
"cdna_length": 7102,
"mane_select": "NM_032223.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000355703.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "n.1363G>T",
"hgvs_p": null,
"transcript": "ENST00000439247.2",
"protein_id": null,
"transcript_support_level": 1,
"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": 3104,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000439247.2"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4730G>T",
"hgvs_p": "p.Arg1577Leu",
"transcript": "ENST00000913358.1",
"protein_id": "ENSP00000583417.1",
"transcript_support_level": null,
"aa_start": 1577,
"aa_end": null,
"aa_length": 2047,
"cds_start": 4730,
"cds_end": null,
"cds_length": 6144,
"cdna_start": 5277,
"cdna_end": null,
"cdna_length": 7153,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913358.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4727G>T",
"hgvs_p": "p.Arg1576Leu",
"transcript": "ENST00000913354.1",
"protein_id": "ENSP00000583413.1",
"transcript_support_level": null,
"aa_start": 1576,
"aa_end": null,
"aa_length": 2046,
"cds_start": 4727,
"cds_end": null,
"cds_length": 6141,
"cdna_start": 5275,
"cdna_end": null,
"cdna_length": 7152,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913354.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4688G>T",
"hgvs_p": "p.Arg1563Leu",
"transcript": "ENST00000913355.1",
"protein_id": "ENSP00000583414.1",
"transcript_support_level": null,
"aa_start": 1563,
"aa_end": null,
"aa_length": 2033,
"cds_start": 4688,
"cds_end": null,
"cds_length": 6102,
"cdna_start": 5236,
"cdna_end": null,
"cdna_length": 7111,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913355.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4688G>T",
"hgvs_p": "p.Arg1563Leu",
"transcript": "ENST00000913359.1",
"protein_id": "ENSP00000583418.1",
"transcript_support_level": null,
"aa_start": 1563,
"aa_end": null,
"aa_length": 2033,
"cds_start": 4688,
"cds_end": null,
"cds_length": 6102,
"cdna_start": 5227,
"cdna_end": null,
"cdna_length": 7102,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913359.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4658G>T",
"hgvs_p": "p.Arg1553Leu",
"transcript": "ENST00000913361.1",
"protein_id": "ENSP00000583420.1",
"transcript_support_level": null,
"aa_start": 1553,
"aa_end": null,
"aa_length": 2023,
"cds_start": 4658,
"cds_end": null,
"cds_length": 6072,
"cdna_start": 5127,
"cdna_end": null,
"cdna_length": 7002,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913361.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4637G>T",
"hgvs_p": "p.Arg1546Leu",
"transcript": "ENST00000913360.1",
"protein_id": "ENSP00000583419.1",
"transcript_support_level": null,
"aa_start": 1546,
"aa_end": null,
"aa_length": 2016,
"cds_start": 4637,
"cds_end": null,
"cds_length": 6051,
"cdna_start": 5164,
"cdna_end": null,
"cdna_length": 7034,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913360.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4598G>T",
"hgvs_p": "p.Arg1533Leu",
"transcript": "ENST00000913356.1",
"protein_id": "ENSP00000583415.1",
"transcript_support_level": null,
"aa_start": 1533,
"aa_end": null,
"aa_length": 2003,
"cds_start": 4598,
"cds_end": null,
"cds_length": 6012,
"cdna_start": 5146,
"cdna_end": null,
"cdna_length": 7021,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913356.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4427G>T",
"hgvs_p": "p.Arg1476Leu",
"transcript": "ENST00000913357.1",
"protein_id": "ENSP00000583416.1",
"transcript_support_level": null,
"aa_start": 1476,
"aa_end": null,
"aa_length": 1946,
"cds_start": 4427,
"cds_end": null,
"cds_length": 5841,
"cdna_start": 4975,
"cdna_end": null,
"cdna_length": 6850,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913357.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4388G>T",
"hgvs_p": "p.Arg1463Leu",
"transcript": "ENST00000913353.1",
"protein_id": "ENSP00000583412.1",
"transcript_support_level": null,
"aa_start": 1463,
"aa_end": null,
"aa_length": 1933,
"cds_start": 4388,
"cds_end": null,
"cds_length": 5802,
"cdna_start": 4946,
"cdna_end": null,
"cdna_length": 6821,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913353.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4730G>T",
"hgvs_p": "p.Arg1577Leu",
"transcript": "XM_011545024.3",
"protein_id": "XP_011543326.1",
"transcript_support_level": null,
"aa_start": 1577,
"aa_end": null,
"aa_length": 2047,
"cds_start": 4730,
"cds_end": null,
"cds_length": 6144,
"cdna_start": 5266,
"cdna_end": null,
"cdna_length": 7141,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011545024.3"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4727G>T",
"hgvs_p": "p.Arg1576Leu",
"transcript": "XM_005273987.6",
"protein_id": "XP_005274044.1",
"transcript_support_level": null,
"aa_start": 1576,
"aa_end": null,
"aa_length": 2046,
"cds_start": 4727,
"cds_end": null,
"cds_length": 6141,
"cdna_start": 5263,
"cdna_end": null,
"cdna_length": 7138,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005273987.6"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4712G>T",
"hgvs_p": "p.Arg1571Leu",
"transcript": "XM_006718549.5",
"protein_id": "XP_006718612.1",
"transcript_support_level": null,
"aa_start": 1571,
"aa_end": null,
"aa_length": 2041,
"cds_start": 4712,
"cds_end": null,
"cds_length": 6126,
"cdna_start": 5248,
"cdna_end": null,
"cdna_length": 7123,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006718549.5"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4709G>T",
"hgvs_p": "p.Arg1570Leu",
"transcript": "XM_047426937.1",
"protein_id": "XP_047282893.1",
"transcript_support_level": null,
"aa_start": 1570,
"aa_end": null,
"aa_length": 2040,
"cds_start": 4709,
"cds_end": null,
"cds_length": 6123,
"cdna_start": 5245,
"cdna_end": null,
"cdna_length": 7120,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426937.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4688G>T",
"hgvs_p": "p.Arg1563Leu",
"transcript": "XM_047426938.1",
"protein_id": "XP_047282894.1",
"transcript_support_level": null,
"aa_start": 1563,
"aa_end": null,
"aa_length": 2033,
"cds_start": 4688,
"cds_end": null,
"cds_length": 6102,
"cdna_start": 5224,
"cdna_end": null,
"cdna_length": 7099,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426938.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.4730G>T",
"hgvs_p": "p.Arg1577Leu",
"transcript": "XM_011545025.4",
"protein_id": "XP_011543327.1",
"transcript_support_level": null,
"aa_start": 1577,
"aa_end": null,
"aa_length": 1844,
"cds_start": 4730,
"cds_end": null,
"cds_length": 5535,
"cdna_start": 5266,
"cdna_end": null,
"cdna_length": 6208,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011545025.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "n.462G>T",
"hgvs_p": null,
"transcript": "ENST00000531280.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 472,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000531280.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"hgvs_c": "c.*202G>T",
"hgvs_p": null,
"transcript": "XM_047426939.1",
"protein_id": "XP_047282895.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1524,
"cds_start": null,
"cds_end": null,
"cds_length": 4575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5213,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426939.1"
}
],
"gene_symbol": "PCNX3",
"gene_hgnc_id": 18760,
"dbsnp": "rs75260332",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7847500443458557,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.262,
"revel_prediction": "Benign",
"alphamissense_score": 0.4925,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.212,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_032223.4",
"gene_symbol": "PCNX3",
"hgnc_id": 18760,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4691G>T",
"hgvs_p": "p.Arg1564Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}