ClinVar Miner

Submissions for variant NM_000455.4(STK11):c.1257C>T (p.Ser419=) (rs375328708)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000213040 SCV000211693 benign not specified 2014-08-19 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Ambry Genetics RCV000160983 SCV000213576 likely benign Hereditary cancer-predisposing syndrome 2015-06-07 criteria provided, single submitter clinical testing
Invitae RCV000473451 SCV000554141 likely benign Peutz-Jeghers syndrome 2017-11-28 criteria provided, single submitter clinical testing
Color RCV000160983 SCV000691482 likely benign Hereditary cancer-predisposing syndrome 2017-03-29 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589957 SCV000696710 benign not provided 2017-04-13 criteria provided, single submitter clinical testing Variant summary: The STK11 c.1257C>T (p.Ser419Ser) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant of interest has been found in a large, broad control population, ExAC in 4/21878 control chromosomes at a frequency of 0.0001828, which is approximately 29 times the estimated maximal expected allele frequency of a pathogenic STK11 variant (0.0000063), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. This variant is co-occuring with a pathogenic variant MSH2 c.366+1G>A in an internal specimen. Taken together, this variant is classified as benign.

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