ClinVar Miner

Submissions for variant NM_001370466.1(NOD2):c.403G>A (p.Val135Ile)

gnomAD frequency: 0.00005  dbSNP: rs139571975
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001782791 SCV000397180 uncertain significance Inflammatory bowel disease 1 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV000295019 SCV000397181 benign Blau syndrome 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Invitae RCV002522853 SCV000958152 likely benign Blau syndrome; Regional enteritis 2023-12-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV002227151 SCV002506216 uncertain significance not provided 2022-01-26 criteria provided, single submitter clinical testing The NOD2 c.484G>A; p.Val162Ile variant (rs139571975), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 319427). This variant is found in the general population with an overall allele frequency of 0.010% (29/281056 alleles) in the Genome Aggregation Database. The valine at codon 162 is weakly conserved, and computational analyses predict that this variant is neutral (REVEL: 0.050). Due to limited information, the clinical significance of this variant is uncertain at this time.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002261055 SCV002542736 likely benign Autoinflammatory syndrome 2021-06-11 criteria provided, single submitter clinical testing

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