ClinVar Miner

Submissions for variant NM_001126049.2(KLLN):c.-1039G>A

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 2023-06-27 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 uncertain significance not specified 2020-04-17 criteria provided, single submitter clinical testing Variant summary: PTEN c.-944C>T (alternatively name c.-943C>T) is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 3.2e-05 in 31296 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.-944C>T in individuals affected with Cowden Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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