ClinVar Miner

Submissions for variant NM_002294.3(LAMP2):c.741+11C>T (rs149155417)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000037426 SCV000061083 benign not specified 2012-11-20 criteria provided, single submitter clinical testing 741+11C>T in intron 5 of LAMP2: This variant is not expected to have clinical si gnificance because it has been identified in 2.1% (9/428) Asian chromosomes from a broad population by the 1000 Genomes project (dbSNP rs149155417).
Illumina Clinical Services Laboratory,Illumina RCV001168183 SCV001330758 benign Danon disease 2018-01-13 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.
Integrated Genetics/Laboratory Corporation of America RCV000037426 SCV001363684 benign not specified 2019-11-04 criteria provided, single submitter clinical testing Variant summary: LAMP2 c.741+11C>T alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.001 in 182348 control chromosomes (gnomAD). The observed variant frequency is approximately 81 fold of the estimated maximal expected allele frequency for a pathogenic variant in LAMP2 causing Cardiomyopathy phenotype (1.3e-05), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.741+11C>T in individuals affected with Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign.

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