ClinVar Miner

Submissions for variant NM_000455.4(STK11):c.96C>G (p.Thr32=) (rs79175212)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000759363 SCV000166364 benign not provided 2019-03-04 criteria provided, single submitter clinical testing
GeneDx RCV000213009 SCV000211691 benign not specified 2014-09-08 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 RCV000160981 SCV000213653 likely benign Hereditary cancer-predisposing syndrome 2015-03-15 criteria provided, single submitter clinical testing
Counsyl RCV000123069 SCV000487860 likely benign Peutz-Jeghers syndrome 2015-11-23 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000213009 SCV000602246 benign not specified 2016-11-23 criteria provided, single submitter clinical testing
Color RCV000160981 SCV000686710 benign Hereditary cancer-predisposing syndrome 2016-05-02 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759363 SCV000888652 benign not provided 2016-11-23 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000213009 SCV000918279 benign not specified 2018-03-28 criteria provided, single submitter clinical testing Variant summary: STK11 c.96C>G 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 variant was observed with an allele frequency of 0.00028 in 275788 control chromosomes (gnomAD). The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 624-folds higher than 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 population(s) of East Asian origin. The variant, c.96C>G, has been reported in the literature in individuals affected with mucinous MDA, breast cancer, and small-intestinal cancer (Kuragaki_2003, Lee_2017, Nakagawa_1999). Nakagawa_1999 indicates that the variant was only present in the tumor sample and not germline. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Multiple ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cites the variant as "likely benign/benign." Based on the evidence outlined above, the variant was classified as benign.

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