ClinVar Miner

Submissions for variant NM_000455.4(STK11):c.1109-5C>T (rs587782020)

Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 7
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000130449 SCV000185313 likely benign Hereditary cancer-predisposing syndrome 2018-06-11 criteria provided, single submitter clinical testing In silico models in agreement (benign);Other strong data supporting benign classification
Invitae RCV000200085 SCV000252699 benign Peutz-Jeghers syndrome 2020-12-01 criteria provided, single submitter clinical testing
Counsyl RCV000200085 SCV000488597 uncertain significance Peutz-Jeghers syndrome 2016-05-03 criteria provided, single submitter clinical testing
Color Health, Inc RCV000130449 SCV000903034 benign Hereditary cancer-predisposing syndrome 2016-07-22 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000780768 SCV000918294 benign not specified 2018-07-13 criteria provided, single submitter clinical testing Variant summary: STK11 c.1109-5C>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, however 5/5 computational tools predict no significant impact on normal splicing. These predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00017 in 267348 control chromosomes (gnomAD). The observed variant frequency is approximately 28-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.1109-5C>T in individuals affected with Peutz-Jeghers Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (2x likely benign/benign, 1x VUS). Based on the evidence outlined above, the variant was classified as benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000780768 SCV001469910 benign not specified 2020-05-04 criteria provided, single submitter clinical testing
GeneDx RCV001711399 SCV001944007 benign not provided 2015-03-03 criteria provided, single submitter clinical testing

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.