ClinVar Miner

Submissions for variant NM_000314.7(PTEN):c.321T>C (p.Asp107=) (rs372876243)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163666 SCV000214238 likely benign Hereditary cancer-predisposing syndrome 2016-02-08 criteria provided, single submitter clinical testing
GeneDx RCV000442474 SCV000514310 likely benign not specified 2018-03-07 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.
Integrated Genetics/Laboratory Corporation of America RCV000590378 SCV000696533 benign not provided 2017-01-10 criteria provided, single submitter clinical testing Variant summary: The PTEN c.321T>C (p.Asp107Asp) variant involves the alteration of a conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 3/121362 control chromosomes at a frequency of 0.0000247, which is approximately 4 times the estimated maximal expected allele frequency of a pathogenic PTEN variant (0.0000063), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. One LCA sample also carried pathogenic variants in BRCA2 c.1796_1800delCTTAT/p.S599X and c.4092_4093insAA/p.C1365fsX10, further supporting the benign classification of this variant. Taken together, this variant is classified as benign.
Invitae RCV000233228 SCV000284588 likely benign PTEN hamartoma tumor syndrome 2017-08-08 criteria provided, single submitter clinical testing

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