ClinVar Miner

Submissions for variant NM_000123.4(ERCC5):c.2877A>C (p.Arg959Ser)

gnomAD frequency: 0.00373  dbSNP: rs41281674
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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 RCV000861337 SCV001001620 benign not provided 2024-01-19 criteria provided, single submitter clinical testing
GeneDx RCV000861337 SCV001825093 likely benign not provided 2020-11-24 criteria provided, single submitter clinical testing
ITMI RCV000120837 SCV000085002 not provided not specified 2013-09-19 no assertion provided reference population
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000861337 SCV001554152 uncertain significance not provided no assertion criteria provided clinical testing The ERCC5 p.Arg959Ser variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs41281674) and ClinVar (classification not provided, submitted by ITMI). The variant was identified in control databases in 360 of 282766 chromosomes (1 homozygous) at a frequency of 0.001273 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 317 of 24960 chromosomes (freq: 0.0127), Other in 7 of 7222 chromosomes (freq: 0.000969), Latino in 30 of 35422 chromosomes (freq: 0.000847), European (Finnish) in 1 of 25122 chromosomes (freq: 0.00004) and European (non-Finnish) in 5 of 129120 chromosomes (freq: 0.000039), but was not observed in the Ashkenazi Jewish, East Asian and South Asian populations. The p.Arg959 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The p.Arg959Ser variant occurs in the third last base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. However, 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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