ClinVar Miner

Submissions for variant NM_000455.4(STK11):c.816C>T (p.Tyr272=) (rs9282859)

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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000129587 SCV000184370 benign Hereditary cancer-predisposing syndrome 2014-11-18 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance;In silico models in agreement (benign);Synonymous alterations with insufficient evidence to classify as benign
PreventionGenetics,PreventionGenetics RCV000241793 SCV000304394 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000333429 SCV000410744 benign Peutz-Jeghers syndrome 2018-01-12 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.
Invitae RCV000333429 SCV000554120 benign Peutz-Jeghers syndrome 2020-12-04 criteria provided, single submitter clinical testing
Color Health, Inc RCV000129587 SCV000686691 benign Hereditary cancer-predisposing syndrome 2015-04-20 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000241793 SCV000884612 benign not specified 2018-07-05 criteria provided, single submitter clinical testing
GeneDx RCV001580067 SCV001895628 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000241793 SCV000692050 benign not specified no assertion criteria provided clinical testing
True Health Diagnostics RCV000129587 SCV000788220 likely benign Hereditary cancer-predisposing syndrome 2018-02-20 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001355314 SCV001550171 benign Malignant tumor of breast no assertion criteria provided clinical testing The STK11 p.Tyr272Tyr variant was not identified in the literature nor was it identified in the MutDB, LOVD 3.0, Zhejiang Colon Cancer Database, and Insight Hereditary Tumors Database databases. The variant was identified in dbSNP (ID: rs9282859) as “Other”, ClinVar (classified benign by Ambry Genetics and Prevention Genetics, and likely benign by Illumina), and in Cosmic (3X all in lung carcinomas). The variant was also identified in control databases in 2204 (84 homozygous) of 273338 chromosomes at a frequency of 0.008 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017), identified in the following populations at a frequency greater than 1%: African in 1993 of 23530 chromosomes (freq: 0.085). The p.Tyr272Tyr 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. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV001580067 SCV001809549 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000241793 SCV001923010 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000241793 SCV001958876 benign not specified no assertion criteria provided clinical testing

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