ClinVar Miner

Submissions for variant NM_000455.4(STK11):c.651G>A (p.Pro217=) (rs368348370)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163335 SCV000213869 likely benign Hereditary cancer-predisposing syndrome 2014-12-18 criteria provided, single submitter clinical testing
Invitae RCV000199595 SCV000253260 likely benign Peutz-Jeghers syndrome 2017-12-01 criteria provided, single submitter clinical testing
GeneDx RCV000434357 SCV000514797 benign not specified 2015-06-29 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.
Color RCV000163335 SCV000537500 likely benign Hereditary cancer-predisposing syndrome 2015-11-12 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000434357 SCV000918280 benign not specified 2017-10-20 criteria provided, single submitter clinical testing Variant summary: The STK11 c.651G>A (p.Pro217Pro) variant involves the alteration of a non-conserved nucleotide located in the protein kinase domain (IPR000719) (InterPro), resulting in a synonymous change. Mutation taster predicts a damaging outcome for this variant. 4/5 splice prediction tools predict no significant impact on normal splicing. ESEfinder predicts that this variant may affect binding of ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 10/263042 control chromosomes at a frequency of 0.000038 (gnomAD), which is approximately 6 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 likely benign/benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories. One internal sample carrying this variant also carried another likely pathogenic variant ATM c.1A>C. Taken together, this variant is classified as benign.

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