Submissions for variant NM_001042492.3(NF1):c.7971-19G>T

gnomAD frequency: 0.01950  dbSNP: rs17887156

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
PreventionGenetics, part of Exact Sciences	RCV000249320	SCV000306299	benign	not specified		criteria provided, single submitter	clinical testing
GeneDx	RCV000587114	SCV000518975	benign	not provided	2016-04-05	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	RCV000587114	SCV000604519	benign	not provided	2023-09-27	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000587114	SCV000696408	benign	not provided	2016-05-12	criteria provided, single submitter	clinical testing	Variant summary: The NF1 c.7908-19G>T variant involves the alteration of a non-conserved intronic nucleotide with 5/5 splice prediction tools calculating no significant effect on splicing, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 699/109636 (21 homozygotes, 1/156, frequency: 0.0063756), predominantly observed in the African cohort, 660/9614 (21 homozygotes, 1/14, frequency: 0.06865), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic NF1 variant of 1/4798 (0.0002084). Therefore, suggesting the variant is a common polymorphism found in population(s) of African origin. The variant of interest, to our knowledge, has not been reported in affected individuals via publications and/or reputable databases/clinical laboratories. Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.
Labcorp Genetics (formerly Invitae), Labcorp	RCV002057433	SCV002457081	benign	Neurofibromatosis, type 1	2025-02-04	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV002057433	SCV002561339	benign	Neurofibromatosis, type 1	2022-03-15	criteria provided, single submitter	clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV003316372	SCV004016407	benign	Neurofibromatosis, familial spinal	2023-07-07	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000249320	SCV001807122	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000249320	SCV001965216	benign	not specified		no assertion criteria provided	clinical testing