ClinVar Miner

Submissions for variant NM_000455.4(STK11):c.552C>T (p.Leu184=) (rs587780719)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000123062 SCV000166357 likely benign Peutz-Jeghers syndrome 2017-12-22 criteria provided, single submitter clinical testing
Ambry Genetics RCV000164592 SCV000215251 likely benign Hereditary cancer-predisposing syndrome 2014-05-22 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000507150 SCV000602229 likely benign not specified 2017-02-20 criteria provided, single submitter clinical testing
Color RCV000164592 SCV000686662 likely benign Hereditary cancer-predisposing syndrome 2015-07-17 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000507150 SCV000918286 benign not specified 2018-02-16 criteria provided, single submitter clinical testing Variant summary: STK11 c.552C>T 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 allele was found at a frequency of 2.3e-05 in 265506 control chromosomes (gnomAD). The observed variant frequency is approximately 3.62 fold of 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 benign. To our knowledge, no occurrence of c.552C>T in individuals affected with Peutz-Jeghers Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as benign.

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