ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.7190-33TTGT[3] (rs149197458)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000247444 SCV000306290 likely benign not specified criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000247444 SCV000604517 benign not specified 2018-07-26 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000247444 SCV000806311 benign not specified 2016-04-22 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000247444 SCV001337821 benign not specified 2020-01-14 criteria provided, single submitter clinical testing Variant summary: NF1 c.7127-19_7127-8del12 (also known as c.7127-19_7127-8delGTTTGTTTGTTT) alters a set of nucleotides 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 0.0025 in 154686 control chromosomes in the gnomAD database, including 4 homozygotes. The observed variant frequency is approximately 12 fold of the estimated maximal expected allele frequency for a pathogenic variant in NF1 causing Neurofibromatosis Type 1 phenotype (0.00021), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.7127-19_7127-8del12 in individuals affected with Neurofibromatosis Type 1 and no experimental evidence demonstrating its impact on protein function have been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (2 as benign, 1 as likely benign; and 1 as a VUS). Based on the evidence outlined above, the variant was classified as benign.
Clinical Genomics Lab,St. Jude Children's Research Hospital RCV000761069 SCV000890984 uncertain significance Neuroblastoma 2016-07-22 no assertion criteria provided clinical testing

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