ClinVar Miner

Submissions for variant NM_004628.5(XPC):c.622-16C>G

gnomAD frequency: 0.02487  dbSNP: rs3731111
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000244980 SCV000310546 benign not specified criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000244980 SCV001360987 benign not specified 2019-10-18 criteria provided, single submitter clinical testing Variant summary: XPC c.622-16C>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 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 0.0075 in 278338 control chromosomes, predominantly at a frequency of 0.081 within the African or African-American subpopulation in the gnomAD database, including 81 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 57 fold of the estimated maximal expected allele frequency for a pathogenic variant in XPC causing Xeroderma pigmentosum phenotype (0.0014), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. To our knowledge, no occurrence of c.622-16C>G in individuals affected with Xeroderma pigmentosum and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign.
GeneDx RCV001675731 SCV001894581 benign not provided 2019-05-20 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002244618 SCV002514018 benign Xeroderma pigmentosum, group C 2021-12-05 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV003316418 SCV004016288 benign Xeroderma pigmentosum group A 2023-07-07 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001675731 SCV004369854 benign not provided 2024-10-08 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV002244618 SCV005880481 benign Xeroderma pigmentosum, group C 2025-02-01 criteria provided, single submitter clinical testing

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