ClinVar Miner

Submissions for variant NM_000355.4(TCN2):c.296A>C (p.Lys99Thr)

gnomAD frequency: 0.00135  dbSNP: rs150225103
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000635260 SCV000756648 likely benign Transcobalamin II deficiency 2024-01-30 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000635260 SCV001309419 uncertain significance Transcobalamin II deficiency 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.
GeneDx RCV001771857 SCV001993854 uncertain significance not provided 2019-05-13 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000635260 SCV004563356 uncertain significance Transcobalamin II deficiency 2023-08-10 criteria provided, single submitter clinical testing The TCN2 c.296A>C; p.Lys99Thr variant (rs150225103), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 529780). This variant is found in the African/African-American population with an allele frequency of 0.38% (96/24,958 alleles) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.209). Due to limited information, the clinical significance of this variant is uncertain at this time.

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