ClinVar Miner

Submissions for variant NM_000455.4(STK11):c.369G>A (p.Gln123=) (rs140112347)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000129594 SCV000184378 benign Hereditary cancer-predisposing syndrome 2014-08-05 criteria provided, single submitter clinical testing This alteration is classified as 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.
Invitae RCV000205529 SCV000261923 benign Peutz-Jeghers syndrome 2020-11-23 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000246390 SCV000304389 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000205529 SCV000410736 likely benign Peutz-Jeghers syndrome 2018-02-08 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Color Health, Inc RCV000129594 SCV000686640 benign Hereditary cancer-predisposing syndrome 2015-04-24 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000246390 SCV001157373 benign not specified 2019-03-27 criteria provided, single submitter clinical testing
GeneDx RCV001354720 SCV001943109 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
True Health Diagnostics RCV000129594 SCV000788218 likely benign Hereditary cancer-predisposing syndrome 2017-10-10 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001354720 SCV001549404 likely benign not provided no assertion criteria provided clinical testing The STK11 p.Gln123= variant was not identified in the literature nor was it identified in the Cosmic, MutDB, LOVD 3.0, Zhejiang Colon Cancer Database, and Insight Hereditary Tumors Database. The variant was identified in dbSNP (ID: rs140112347) as “other”, ClinVar (classified as benign/likely benign; submitters: benign by Ambry Genetics, Invitae and Prevention Genetics; likely benign by Illumina Clinical Services Laboratory) and in control databases in 563 (8 homozygous) of 277056 chromosomes at a frequency of 0.002 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017), identified in the following population at a frequency greater than 1%: African in 515 (8 homozygous) of 24002 chromosomes (freq: 0.02) . The p.Gln123= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. The variant occurs 6 nucleotides from the end of exon 2 and and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000246390 SCV001808920 benign not specified no assertion criteria provided clinical testing
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C. RCV000129594 SCV001950170 benign Hereditary cancer-predisposing syndrome 2021-09-15 no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV001354720 SCV001955658 likely benign not provided no assertion criteria provided clinical testing

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