ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.7410T>C (p.Asn2470=)

gnomAD frequency: 0.00067  dbSNP: rs17881903
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163438 SCV000213985 likely benign Hereditary cancer-predisposing syndrome 2014-09-12 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Invitae RCV000205235 SCV000261768 benign Neurofibromatosis, type 1 2020-11-24 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000504397 SCV000595975 likely benign not specified 2016-08-24 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000504397 SCV000917887 benign not specified 2018-01-29 criteria provided, single submitter clinical testing Variant summary: NF1 c.7347T>C (p.Asn2449=) alters a non-conserved nucleotide resulting in a synonymous change. 5/5 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 (58/24034 chrs) database is approximately 11.52 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 a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.7347T>C in individuals affected with Neurofibromatosis Type 1 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. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.
GeneDx RCV001589023 SCV001827164 likely benign not provided 2021-08-02 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001589023 SCV002048939 benign not provided 2021-03-13 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000163438 SCV002528100 benign Hereditary cancer-predisposing syndrome 2021-05-30 criteria provided, single submitter curation
Genome-Nilou Lab RCV000205235 SCV002561291 likely benign Neurofibromatosis, type 1 2022-03-15 criteria provided, single submitter clinical testing

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