ClinVar Miner

Submissions for variant NM_001164508.2(NEB):c.6491G>A (p.Ser2164Asn)

gnomAD frequency: 0.00013  dbSNP: rs780626863
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002548514 SCV003299015 likely benign Nemaline myopathy 2 2024-01-18 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV001356511 SCV003812210 uncertain significance not provided 2023-05-25 criteria provided, single submitter clinical testing
GeneDx RCV001356511 SCV003936668 uncertain significance not provided 2022-12-29 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001356511 SCV001551708 uncertain significance not provided no assertion criteria provided clinical testing The NEB p.Ser2164Asn variant was not identified in the literature nor was it found in ClinVar or LOVD 3.0. The variant was identified in dbSNP (ID: rs780626863) and in control databases in 20 of 260708 chromosomes at a frequency of 0.00007671 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Other in 1 of 6594 chromosomes (freq: 0.000152), European (non-Finnish) in 16 of 120198 chromosomes (freq: 0.000133) and Latino in 3 of 34144 chromosomes (freq: 0.000088), but was not observed in the African, Ashkenazi Jewish, East Asian, European (Finnish), or South Asian populations. The p.Ser2164 residue is conserved across mammals and other organisms however computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein. The variant occurs outside of the splicing consensus sequence and three of four 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. This variant is classified as a variant of uncertain significance.

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