ClinVar Miner

Submissions for variant NM_000314.6(PTEN):c.165-13_165-10delGTTT (rs786204877)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen PTEN Variant Curation Expert Panel RCV000710297 SCV000840473 likely benign PTEN hamartoma tumor syndrome 2016-12-14 reviewed by expert panel curation PTEN c.165-13_165-10delGTTT (IVS2-13_IVS2-10delGTTT) meets criteria to be classified as likely benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (Mester et al. 2018; manuscript in preparation). Please see a summary of the rules and criteria codes in the 'PTEN ACMG Specifications Summary' document (assertion method column). BS1: Allele frequency of 0.0049 (0.49%, 112/22,776 alleles) in the African subpopulation of the gnomAD cohort. (PMID 27535533) BP4: Intronic variant where at least 2 out of 3 in silico models predict no splicing impact.
GeneDx RCV000169818 SCV000222137 benign Hereditary cancer-predisposing syndrome 2014-10-09 criteria provided, single submitter clinical testing The variant is found in BR-OV-HEREDIC panel(s).
PreventionGenetics,PreventionGenetics RCV000244062 SCV000303570 likely benign not specified criteria provided, single submitter clinical testing
Counsyl RCV000409424 SCV000489369 likely benign Cowden syndrome 1 2016-09-26 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000244062 SCV000604972 benign not specified 2016-10-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587583 SCV000696531 benign not provided 2016-10-14 criteria provided, single submitter clinical testing Variant summary: The PTEN c.165-13_165-10delGTTT variant involves a deletion of four nucleotides located in intron 2. Mutation taster predicts a disease causing outcome while 5/5 splice site prediction tools predict the variant not to have an impact on splicing. This variant was found in 40/87010 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.0048202 (37/7676). This frequency greatly exceeds the estimated maximal expected allele frequency of a pathogenic PTEN variant (0.0000063), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases; nor evaluated for functional impact by in vivo/vitro studies. Based on the high prevalence of the variant in the general population it was classified as benign.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000244062 SCV000707311 likely benign not specified 2017-04-03 criteria provided, single submitter clinical testing

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