ClinVar Miner

Submissions for variant NM_000455.5(STK11):c.-2G>T

gnomAD frequency: 0.00003  dbSNP: rs774072752
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000288357 SCV000410732 benign Peutz-Jeghers syndrome 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
GeneDx RCV000436151 SCV000514789 benign not specified 2015-06-17 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 RCV000492081 SCV000580942 likely benign Hereditary cancer-predisposing syndrome 2020-09-04 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000436151 SCV000602220 benign not specified 2021-08-09 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000586834 SCV000696714 benign not provided 2016-06-27 criteria provided, single submitter clinical testing Variant summary: The STK11 c.-2G>T variant is located in the 5'UTR involving a conserved nucleotide with 5/5 splice prediction tools predicting no significant impact on splicing and alterations to ESE binding, although these predictions have yet to be functionally assesed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 6/24392 (1/4065), predominantly in the Latino cohort, 6/916 (1/152), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic STK11 variant of 1/158730. Therefore, suggesting the variant of interest is a common polymorphism found in population(s) of Latino origin. The variant of interest was has not been, to our knowledge, reported in affected individuals via publications and/or reputable databases/clinical laboratories. However, an internal LCA specimen reports the variant to co-occur with another potentially pathogenic MLH1 variant, c.1731+1G>T (scored "likely pathogenic"). Therefore, taking all available lines of evidence into consideration, the variant of interest has been classified as Benign.
PreventionGenetics, PreventionGenetics RCV000586834 SCV000806066 likely benign not provided 2017-07-28 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000492081 SCV000903058 likely benign Hereditary cancer-predisposing syndrome 2015-04-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000288357 SCV002057223 benign Peutz-Jeghers syndrome 2021-07-15 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000436151 SCV002072420 uncertain significance not specified 2019-07-01 criteria provided, single submitter clinical testing

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