ClinVar Miner

Submissions for variant NM_006767.4(LZTR1):c.652-10C>A

gnomAD frequency: 0.00049  dbSNP: rs200169897
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001260420 SCV001437412 benign not specified 2020-09-08 criteria provided, single submitter clinical testing Variant summary: LZTR1 c.652-10C>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00056 in 251174 control chromosomes, predominantly at a frequency of 0.00057 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 114 fold of the estimated maximal expected allele frequency for a pathogenic variant in LZTR1 causing Noonan Syndrome phenotype (5e-06), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. To our knowledge, no occurrence of c.652-10C>A in individuals affected with Noonan Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV001519192 SCV001728019 benign not provided 2025-02-02 criteria provided, single submitter clinical testing
GeneDx RCV001519192 SCV001802510 likely benign not provided 2020-08-04 criteria provided, single submitter clinical testing
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV001519192 SCV002009527 uncertain significance not provided 2021-11-03 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV005360003 SCV005914436 likely benign LZTR1-related schwannomatosis 2022-08-17 criteria provided, single submitter clinical testing

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