ClinVar Miner

Submissions for variant NM_001126049.2(KLLN):c.-794_-783del (rs587781340)

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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 RCV000790891 SCV000930127 likely benign PTEN hamartoma tumor syndrome 2019-03-05 reviewed by expert panel curation PTEN c.-1195del12 (NC_000010.10:g.89623031_89623042delAAGCCGCAGCAA) meets criteria to be classified as likely benign 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). BS4_P: Lack of segregation in affected members of one family. (Internal laboratory contributor SCV SCV000222146.7) BP5: Variant found in multiple cases with alternate molecular basis for disease. (Internal laboratory contributors SCV000222146.7, SCV000183826.5)
Ambry Genetics RCV000129113 SCV000183826 likely benign Hereditary cancer-predisposing syndrome 2019-07-24 criteria provided, single submitter clinical testing Co-occurence with a mutation in another gene that clearly explains a proband's phenotype;Co-occurence with mutation in same gene (phase unknown);Other data supporting benign classification
GeneDx RCV000506666 SCV000222146 uncertain significance not provided 2018-09-19 criteria provided, single submitter clinical testing This variant is denoted PTEN c.-1196_-1185del12, and describes a deletion of 12 nucleotides located 1196 base pairs upstream of the ATG translocation state site in the PTEN core promoter region. The surrounding sequence, with the bases that are deleted in brackets, is GCAA[del12]GTGC. This deletion has been reported previously using alternative numbering (c.-1195del12, based on GRCh36/UCSC hg18) in at least two individuals with breast and/or thyroid cancer, neither of whom met full International Cowden Syndrome Consortium operational criteria (Tan 2011, Wang 2011). PTEN c.-1196_-1185del12 is reported to overlap the androgen receptor-binding element (ARE) in the PTEN promoter and has been shown to modify androgen-mediated PTEN transcriptional activity in breast cancer and prostate cancer cell lines (Wang 2011). Based on currently available information, it is unclear whether PTEN c.-1196_-1185del12 is pathogenic or benign. We consider it to be a variant of uncertain significance.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000506666 SCV000602111 likely benign not provided 2020-12-29 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000506666 SCV001148032 likely benign not provided 2020-08-01 criteria provided, single submitter clinical testing

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