ClinVar Miner

Submissions for variant NM_000314.8(PTEN):c.-944C>T

gnomAD frequency: 0.00004  dbSNP: rs587779999
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Clingen PTEN Variant Curation Expert Panel, Clingen RCV002286568 SCV002576573 uncertain significance PTEN hamartoma tumor syndrome 2020-10-20 reviewed by expert panel curation PTEN c.-943C>T (NC_000010.10:g.89623283C>T) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). No criteria currently apply to this variant.
GeneDx RCV000258977 SCV000149486 uncertain significance not provided 2024-02-05 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; Not observed at significant frequency in large population cohorts (gnomAD); Also known as c.-943C>T
Ambry Genetics RCV000115577 SCV000187185 uncertain significance Hereditary cancer-predisposing syndrome 2014-03-25 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000763681 SCV000894561 uncertain significance Macrocephaly-autism syndrome; Familial meningioma; Malignant tumor of prostate; VACTERL with hydrocephalus; Glioma susceptibility 2; PTEN hamartoma tumor syndrome; Cowden syndrome 1 2018-10-31 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001175018 SCV001338534 likely benign not specified 2024-09-09 criteria provided, single submitter clinical testing Variant summary: PTEN c.-944C>T is located in the untranscribed region upstream of the PTEN gene region. The variant allele was found at a frequency of 6e-05 in 383106 control chromosomes, predominantly at a frequency of 9.2e-05 within the Non-Finnish European subpopulation in the gnomAD database (v4.1 dataset). The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 5.9-fold of the estimated maximal expected allele frequency for a pathogenic variant in PTEN causing Hereditary Breast And Ovarian Cancer Syndrome phenotype (1.6e-05). The variant, c.-944C>T, has been reported in the literature in an individual affected with breast- and/or ovarian cancer (Guglielmi_2021), and although patients I this cohort had positive family history for the disease, no supporting evidence for causality for this variant was provided. This report does not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 34299313). ClinVar contains an entry for this variant (Variation ID: 127682). Based on the evidence outlined above, the variant was classified as likely benign.

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