ClinVar Miner

Submissions for variant NM_001126049.2(KLLN):c.-898G>A (rs538728843)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen PTEN Variant Curation Expert Panel RCV000229583 SCV000886872 likely benign PTEN hamartoma tumor syndrome 2018-11-28 reviewed by expert panel curation PTEN c.-1084C>T (NC_000010.10:g.89623142C>T) 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). BS1: Allele frequency of 0.0025 (0.25%, 38/14,966 alleles) in the European subpopulation of the gnomAD cohort. (PMID 27535533) BP2: At least three observations in cis and/or phase unknown with different pathogenic/likely pathogenic PTEN variants. (internal laboratory contributor(s) SCV000149464.4) BS2_P: Meets criteria for BS2 (observed in the homozygous state in at least one healthy or PHTS-unaffected individual) but BS1 is also applied. (PMID 27884173, internal laboratory contributor(s) SCV000149464.4, SCV000185343.1)
GeneDx RCV000201312 SCV000149464 likely benign not specified 2015-05-07 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. This variant was found in HIBR-PALB2-HEREDIC,BR-OV-HEREDIC,BR-GUIDE-HEREDIC,HEREDICANCER,PTEN-HEREDIC,ALACARTE-HEREDIC,MACRO-BRAIN,HIRISK-BR-HEREDIC,COLO-HEREDIC,ENDOM-HEREDIC,COLYNCH-HEREDICV3-REST,COLOV2-HEREDIC,PTEN,MODRISK-HEREDIC
Ambry Genetics RCV000115555 SCV000185343 uncertain significance Hereditary cancer-predisposing syndrome 2013-12-18 criteria provided, single submitter clinical testing
Invitae RCV000229583 SCV000284570 benign PTEN hamartoma tumor syndrome 2016-03-31 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000201312 SCV000540135 uncertain significance not specified 2016-03-28 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Region not covered by ExAC,reported in 1 proband, analysis of patient samples suggests possible impact to PTEN expression, but insufficient evidence for pathogenicity.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000201312 SCV000604971 likely benign not specified 2016-12-15 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000586614 SCV000696525 benign not provided 2017-02-09 criteria provided, single submitter clinical testing Variant summary: The PTEN variant c.-1084C>T (also known as c.-1085C>T) involves the alteration of a non-conserved nucleotide in the 5'UTR region. One in silico tool predicts a benign outcome for this variant. This variant was found in 28/5008 control chromosomes, predominantly observed in South Asians at a frequency of 0.0163599 (16/978). 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 origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign/benign. Taken together, this variant is classified as benign.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000586614 SCV000780347 likely benign not provided 2018-01-01 criteria provided, single submitter clinical testing
Counsyl RCV000662713 SCV000785463 likely benign Cowden syndrome 1 2017-08-14 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000201312 SCV000860984 benign not specified 2018-04-24 criteria provided, single submitter clinical testing
Mendelics RCV000229583 SCV001138115 benign PTEN hamartoma tumor syndrome 2019-05-28 criteria provided, single submitter clinical testing

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