ClinVar Miner

Submissions for variant NM_000455.5(STK11):c.357C>T (p.Asn119=)

gnomAD frequency: 0.00003  dbSNP: rs372511774
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000213010 SCV000211678 benign not specified 2014-01-23 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 RCV000160969 SCV000213678 likely benign Hereditary cancer-predisposing syndrome 2014-10-22 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.
Eurofins NTD LLC (GA) RCV000590217 SCV000227128 uncertain significance not provided 2015-04-10 criteria provided, single submitter clinical testing
Invitae RCV000195629 SCV000253249 benign Peutz-Jeghers syndrome 2021-12-17 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV000195629 SCV000410735 uncertain significance 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Counsyl RCV000195629 SCV000488905 likely benign Peutz-Jeghers syndrome 2016-07-18 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000160969 SCV000686637 likely benign Hereditary cancer-predisposing syndrome 2015-05-18 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000590217 SCV000696716 benign not provided 2016-09-30 criteria provided, single submitter clinical testing Variant summary: The STK11 c.357C>T (p.Asn119Asn) variant causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools predicting no significant impact on normal splicing. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 10/120328 (1/12032), which is approximately 13 times the estimated maximal expected allele frequency for a pathogenic STK11 variant 1/158730 (0.0000063), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories have classified this variant as benign/likely benign. One internal sample carrying this variant also carries another likely pathogenic variant RAD51C c.93delG, further supporting the benign outcome. Taken together, this variant is classified as Benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000213010 SCV001469914 benign not specified 2020-04-20 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000590217 SCV001473727 likely benign not provided 2019-11-24 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000195629 SCV002057237 likely benign Peutz-Jeghers syndrome 2021-07-15 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000213010 SCV002065598 likely benign not specified 2020-12-18 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000160969 SCV002531685 benign Hereditary cancer-predisposing syndrome 2021-04-29 criteria provided, single submitter curation

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