Submissions for variant NM_001042492.3(NF1):c.2851-16T>C

gnomAD frequency: 0.01543  dbSNP: rs17880825

Total submissions: 15

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
PreventionGenetics, part of Exact Sciences	RCV000246512	SCV000306250	benign	not specified		criteria provided, single submitter	clinical testing
GeneDx	RCV000587446	SCV000518954	benign	not provided	2017-07-05	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.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000587446	SCV000604475	benign	not provided	2023-11-09	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000587446	SCV000696391	benign	not provided	2016-05-11	criteria provided, single submitter	clinical testing	Variant summary: The NF1 c.2851-16T>C variant involves the alteration of a non-conserved intronic nucleotide. 5/5 programs in Alamut predict that this variant does not affect normal splicing, however no functional studies supporting this notion were published at the time of evaluation. This variant was found in 2130/121080 control chromosomes (29 homozygotes), predominantly observed in the European (Non-Finnish), subpopulation at a frequency of 0.0253362 (1688/66624). This frequency is about 122 times the estimated maximal expected allele frequency of a pathogenic NF1 variant (0.0002084), suggesting this is likely a benign polymorphism found primarily in the populations of European (Non-Finnish) descent. In addition, the variant of interest was found to co-occur with known pathogenic mutation, c.3528delA (p.L1183*) in NF1 gene in a patient with a clinical diagnosis of neurofibromatosis. Taken together, based on the prevalence in general population, this variant was classified as Benign.
Athena Diagnostics	RCV000246512	SCV001476705	benign	not specified	2020-04-10	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV002057431	SCV002403975	benign	Neurofibromatosis, type 1	2024-02-01	criteria provided, single submitter	clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000246512	SCV002550890	benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV002057431	SCV002560621	benign	Neurofibromatosis, type 1	2022-03-15	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002436081	SCV002748169	benign	Hereditary cancer-predisposing syndrome; Cardiovascular phenotype	2014-07-14	criteria provided, single submitter	clinical testing	This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, 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.
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV003316360	SCV004016399	benign	Neurofibromatosis, familial spinal	2023-07-07	criteria provided, single submitter	clinical testing
Breakthrough Genomics, Breakthrough Genomics	RCV000587446	SCV005253773	benign	not provided		criteria provided, single submitter	not provided
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000246512	SCV001808255	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000246512	SCV001957828	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000246512	SCV001973122	benign	not specified		no assertion criteria provided	clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV000246512	SCV002037042	benign	not specified		no assertion criteria provided	clinical testing