ClinVar Miner

Submissions for variant NM_000251.2(MSH2):c.2006-2A>G (rs267607991)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color RCV000774579 SCV000908323 likely pathogenic Hereditary cancer-predisposing syndrome 2018-08-09 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000076349 SCV000917706 pathogenic Lynch syndrome 2018-11-08 criteria provided, single submitter clinical testing Variant summary: MSH2 c.2006-2A>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Five predict the variant abolishes a 3 acceptor site. These predictions are supported by a functional study, Ding_2007, which indicates the variant causes exon 13 skipping. The variant was absent in 246132 control chromosomes (gnomAD). c.2006-2A>G has been reported in the literature in individuals affected with Lynch Syndrome including a de novo occurrence (Ding_2007, Morak_2017, Parc_2003). These data indicate that the variant may be associated with disease. 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 pathogenic.
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) RCV000076349 SCV000107375 likely pathogenic Lynch syndrome 2013-09-05 reviewed by expert panel research Interrupts canonical acceptor splice site (splicing tested in tumour sample only)

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