ClinVar Miner

Submissions for variant NM_000314.8(PTEN):c.210-12C>T

gnomAD frequency: 0.00001  dbSNP: rs766570103
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000663280 SCV000786517 likely benign Cowden syndrome 1 2018-05-17 criteria provided, single submitter clinical testing
GeneDx RCV000827092 SCV000968709 likely benign not provided 2018-05-06 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.
Color Diagnostics, LLC DBA Color Health RCV001525142 SCV001735182 likely benign Hereditary cancer-predisposing syndrome 2020-10-30 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002060803 SCV002356196 likely benign PTEN hamartoma tumor syndrome 2023-09-01 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV001525142 SCV002528225 likely benign Hereditary cancer-predisposing syndrome 2022-01-13 criteria provided, single submitter curation
Myriad Genetics, Inc. RCV000663280 SCV004019932 likely benign Cowden syndrome 1 2023-04-05 criteria provided, single submitter clinical testing This variant is considered likely benign. This variant is intronic and is not expected to impact mRNA splicing.
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001354121 SCV001548660 likely benign Carcinoma of colon no assertion criteria provided clinical testing The PTEN c.210-12C>T variant was not identified in the literature nor was it identified in the LOVD 3.0 database. The variant was identified in dbSNP (rs766570103) as “with likely benign allele and ClinVar (classified as likely benign by Counsyl). The variant was identified in control databases in 2 of 280,598 chromosomes at a frequency of 0.000007 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Other in 1 of 7150 chromosomes (freq: 0.0001), Latino in 1 of 35,198 chromosomes (freq: 0.00003), while the variant was not observed in the African, Ashkenazi Jewish, East Asian, Finnish, European, and South Asian populations. The c.210-12C>T variant is located at a non-highly conserved nucleotide 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. 4 out of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) 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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