ClinVar Miner

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

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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 RCV000130449 SCV000185313 likely benign Hereditary cancer-predisposing syndrome 2017-04-19 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: In silico models in agreement (benign),Other strong data supporting benign classification
Color RCV000130449 SCV000903034 benign Hereditary cancer-predisposing syndrome 2016-07-22 criteria provided, single submitter clinical testing
Counsyl RCV000200085 SCV000488597 uncertain significance Peutz-Jeghers syndrome 2016-05-03 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America 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.
Invitae RCV000200085 SCV000252699 benign Peutz-Jeghers syndrome 2017-11-20 criteria provided, single submitter clinical testing

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