ClinVar Miner

Submissions for variant NM_000455.5(STK11):c.920+7G>T

dbSNP: rs2075607
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001083565 SCV000166362 likely benign Peutz-Jeghers syndrome 2023-11-24 criteria provided, single submitter clinical testing
GeneDx RCV000438894 SCV000517971 likely benign not specified 2017-04-19 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000438894 SCV000696734 likely benign not specified 2021-07-23 criteria provided, single submitter clinical testing Variant summary: STK11 c.920+7G>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 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 5.9e-06 in 170686 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. However, a different nucleotide change at the same location, namely c.920+7G>C (19-1222012-G -C) is present at a frequency of 18% in the gnomAD database, thereby suggesting that this position is likely to be tolerant. To our knowledge, no occurrence of c.920+7G>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. All laboratories classified the variant as likely benign. Based on the evidence outlined above, the variant was re-classified as likely benign.
Color Diagnostics, LLC DBA Color Health RCV000775660 SCV000910054 likely benign Hereditary cancer-predisposing syndrome 2018-08-07 criteria provided, single submitter clinical testing

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