ClinVar Miner

Submissions for variant NM_000455.4(STK11):c.723T>C (p.Ala241=) (rs533550278)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000858702 SCV000166361 benign not provided 2019-02-14 criteria provided, single submitter clinical testing
Ambry Genetics RCV000163237 SCV000213764 likely benign Hereditary cancer-predisposing syndrome 2014-08-05 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000123066 SCV000410742 likely benign Peutz-Jeghers syndrome 2016-06-14 criteria provided, single submitter clinical testing
Counsyl RCV000123066 SCV000487841 likely benign Peutz-Jeghers syndrome 2015-11-20 criteria provided, single submitter clinical testing
GeneDx RCV000418469 SCV000517834 likely benign not specified 2017-04-24 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 RCV000163237 SCV000686678 likely benign Hereditary cancer-predisposing syndrome 2015-04-29 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000418469 SCV000918287 benign not specified 2018-05-21 criteria provided, single submitter clinical testing Variant summary: STK11 c.723T>C alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 368 fold above the estimated maximal expected allele frequency for a pathogenic variant in STK11 causing Peutz-Jeghers Syndrome phenotype (6.3e-06), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. To our knowledge, no occurrence of c.723T>C in individuals affected with Peutz-Jeghers Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.

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