Submissions for variant NM_001271208.2(NEB):c.9052G>A (p.Asp3018Asn) (rs192098032)

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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	RCV000244749	SCV000307400	benign	not specified		criteria provided, single submitter	clinical testing
GeneDx	RCV000244749	SCV000532131	benign	not specified	2016-11-15	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.
Invitae	RCV001080599	SCV000640887	benign	Nemaline myopathy 2	2019-12-31	criteria provided, single submitter	clinical testing
Integrated Genetics/Laboratory Corporation of America	RCV000588460	SCV000697843	benign	not provided	2017-04-24	criteria provided, single submitter	clinical testing	Variant summary: The c.9052G>A (p.Asp3018Asn) in NEB gene is a missense change that alters a conserved nucleotide and 4/4 in silico tools predict damaging outcome. The variant is located within conserved nebulin repeats, although the impact of this change is yet to be confirmed by functional studies. The variant is present in the large control population datasets of ExAC and gnomAD at similar frequency (264/117446 chrs and 668/274324 chrs, respectively), predominantly East Asian sub-population [0.0310 (257/8286 chrs) in ExAC and 0.03452 (648/18770 chrs tested, including 10 homozygotes) in gnomAD]. These frequencies exceed the estimated maximal expected allele frequency of a pathogenic variant in NEB gene (0.0035). This variant has been reported in two siblings from a family with nemaline myopathy in compound heterozygous state with p.Ser8228Ser (Chen_2013); whether this genotype explained the phenotype in the family is unknown. Lastly, a reputable database/diagnostic center has classified the variant of interest as benign. Taken together, the variant was classified as Benign.
Athena Diagnostics Inc	RCV000588460	SCV001144732	benign	not provided	2019-06-27	criteria provided, single submitter	clinical testing

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