ClinVar Miner

Submissions for variant NM_000455.4(STK11):c.598-8C>T (rs373610101)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001083841 SCV000166358 benign Peutz-Jeghers syndrome 2020-12-04 criteria provided, single submitter clinical testing
Ambry Genetics RCV000131148 SCV000186088 likely benign Hereditary cancer-predisposing syndrome 2015-01-22 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.
GeneDx RCV000213015 SCV000211683 benign not specified 2014-08-15 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.
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C. RCV000131148 SCV000576426 likely benign Hereditary cancer-predisposing syndrome 2017-02-14 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000213015 SCV000602233 likely benign not specified 2017-04-13 criteria provided, single submitter clinical testing
Color Health, Inc RCV000131148 SCV000686669 benign Hereditary cancer-predisposing syndrome 2015-11-17 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000589505 SCV000696724 benign not provided 2016-01-25 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000589505 SCV000889862 benign not provided 2018-04-13 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001355241 SCV001550067 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The STK11 c.598-8C>T variant was not identified in the literature nor was it identified in the Cosmic, MutDB, LOVD 3.0, Zhejiang Colon Cancer Database, or Insight Hereditary Tumors Database. The variant was identified in dbSNP (ID: rs373610101) as “With Likely benign allele”, ClinVar (as benign by Invitae, GeneDx, Color Genomics, and Laboratory Corporation of America, and as likely benign by Ambry Genetics, Institute for Biomarker Research, and Quest Diagnostics), and Clinvitae (as in ClinVar) databases. The variant was identified in control databases in 97 of 222910 chromosomes at a frequency of 0.000435 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include African in 82 of 19170 chromosomes (freq: 0.004278), Latino in 5 of 29260 chromosomes (freq: 0.000171), European (Non-Finnish) in 10 of 97440 chromosomes (freq: 0.000103), while the variant was not observed in the Other, Ashkenazi Jewish, East Asian, European (Finnish), and South Asian populations. The c.598-8C>T variant is located in the 3' splice region but does not affect the invariant -1 and -2 positions. However, positions -3 and -5 to -12 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. However, 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 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 RCV000589505 SCV001808470 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000589505 SCV001918567 likely benign not provided no assertion criteria provided clinical testing

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