ClinVar Miner

Submissions for variant NM_016418.5(NF2):c.1123-6C>T (rs147898623)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000234108 SCV000284540 benign Neurofibromatosis, type 2 2020-11-26 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000234108 SCV000437753 likely benign Neurofibromatosis, type 2 2016-06-14 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000732056 SCV000859934 uncertain significance not provided 2018-03-13 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000780549 SCV000917897 benign not specified 2018-05-03 criteria provided, single submitter clinical testing Variant summary: NF2 c.1123-6C>T 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. 4/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The observed variant frequency within African control individuals in the gnomAD database is approximately 337.92 fold of the estimated maximal expected allele frequency for a pathogenic variant in NF2 causing Neurofibromatosis Type 2 phenotype (1.9e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.1123-6C>T in individuals affected with Neurofibromatosis Type 2 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, and classified the variant as benign/likely benign. Another lab classified this variant as VUS, also without evidence for independent evaluation. Based on the evidence outlined above, the variant was classified as benign.
GeneDx RCV000732056 SCV001826533 likely benign not provided 2021-03-29 criteria provided, single submitter clinical testing

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