ClinVar Miner

Submissions for variant NM_000314.7(PTEN):c.802-12T>C (rs587781129)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000127651 SCV000171230 benign not specified 2014-02-06 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.
Counsyl RCV000410996 SCV000489513 likely benign Cowden syndrome 1 2016-10-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001108875 SCV001266162 benign PTEN hamartoma tumor 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.
Color Health, Inc RCV001190642 SCV001358193 likely benign Hereditary cancer-predisposing syndrome 2019-11-05 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001108875 SCV001552018 likely benign PTEN hamartoma tumor syndrome no assertion criteria provided clinical testing The PTEN c.802-12T>C variant was not identified in the literature nor was it identified in the following databases: Cosmic, MutDB, LOVD 3.0, or Zhejiang Colon Cancer Database. The variant was identified in the databases: dbSNP (ID: rs587781129) as "With Likely benign allele", and ClinVar/Clinvitae (2x, benign/likely benign). The variant was identified in control databases in 51 of 204652 chromosomes at a frequency of 0.0002 increasing the likelihood that this may be a low frequency benign variant in certain populations of origin (Genome Aggregation Consortium Feb 27, 2017). Of note, in the Ashkenazi Jewish population the variant was identified in 40 of 8652 chromosomes (freq. 0.005). The c.802-12T>C 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. Conversely, 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.

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