ClinVar Miner

Submissions for variant NM_004628.5(XPC):c.2061G>A (p.Arg687=)

gnomAD frequency: 0.26212  dbSNP: rs2227998
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000122327 SCV000310537 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000314393 SCV000441369 benign Xeroderma pigmentosum, group C 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV001513522 SCV001721150 benign not provided 2025-01-30 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000122327 SCV001737748 benign not specified 2021-06-16 criteria provided, single submitter clinical testing Variant summary: XPC c.2061G>A results in a synonymous change. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.25 in 245744 control chromosomes in the gnomAD database, including 8333 homozygotes. The observed variant frequency is approximately 357 fold of the estimated maximal expected allele frequency for a pathogenic variant in XPC causing Xeroderma Pigmentosum phenotype (0.00071), strongly suggesting that the variant is benign. The variant c.2061G>A, has been reported in the literature (example: PMID: 27285993, 10766188). One ClinVar submitter (evaluation after 2014) cites the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
GeneDx RCV001513522 SCV001882116 benign not provided 2019-01-10 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000314393 SCV002514000 benign Xeroderma pigmentosum, group C 2021-12-05 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV003315790 SCV004016280 benign Xeroderma pigmentosum group A 2023-07-07 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV001513522 SCV005241619 benign not provided criteria provided, single submitter not provided
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV000314393 SCV005880484 benign Xeroderma pigmentosum, group C 2025-02-01 criteria provided, single submitter clinical testing
ITMI RCV000122327 SCV000086557 not provided not specified 2013-09-19 no assertion provided reference population

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