ClinVar Miner

Submissions for variant NM_021076.4(NEFH):c.2601G>T (p.Lys867Asn)

gnomAD frequency: 0.00178  dbSNP: rs138156220
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000972353 SCV001120058 benign not provided 2024-01-28 criteria provided, single submitter clinical testing
Ambry Genetics RCV002434331 SCV002745495 likely benign Inborn genetic diseases 2019-11-15 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.
PreventionGenetics, part of Exact Sciences RCV003960849 SCV004767264 likely benign NEFH-related condition 2023-04-12 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000972353 SCV001550188 likely benign not provided no assertion criteria provided clinical testing The NEFH p.Lys867Asn variant was identified in 1 of 380 proband chromosomes (frequency: 0.0026) from individuals with amyotrophic lateral sclerosis and was not identified in 380 control chromosomes from healthy individuals (Daoud_2011_PMID:21220648). The variant was identified in dbSNP (ID: rs138156220) and ClinVar (classified as benign by Invitae). The variant was identified in control databases in 144 of 274484 chromosomes at a frequency of 0.0005246 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: African in 122 of 24320 chromosomes (freq: 0.005016), Latino in 21 of 34474 chromosomes (freq: 0.000609) and East Asian in 1 of 19360 chromosomes (freq: 0.000052), but was not observed in the Ashkenazi Jewish, European (Finnish), European (non-Finnish), Other, or South Asian populations. The p.Lys867 residue is conserved in mammals and four of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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