ClinVar Miner

Submissions for variant NM_000492.3(CFTR):c.1584+53_1584+63dup (rs397508232)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000507332 SCV000601050 uncertain significance not specified 2017-03-14 criteria provided, single submitter clinical testing
Invitae RCV000533542 SCV000625727 benign Cystic fibrosis 2020-11-21 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000507332 SCV000919161 benign not specified 2018-10-25 criteria provided, single submitter clinical testing Variant summary: CFTR c.1584+53_1584+63dup11 is located at a deep intronic position not widely known to affect splicing. 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 0.00088 in 259470 control chromosomes, predominantly within the African subpopulation in the gnomAD database at a frequency of 0.0086, including 1 homozygote. The observed variant frequency within African control individuals is approximately 1.5-fold above the estimated maximal expected allele frequency for a pathogenic variant in CFTR causing Chronic Pancreatitis Risk phenotype (0.0063), suggesting that the variant is a benign polymorphism found primarily in populations of African origin. c.1584+53_1584+63dup11 has been reported in the literature without evidence for pathogenicity, thus these reports do not provide unequivocal conclusions about association of the variant with Chronic Pancreatitis Risk. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as benign, and one laboratory classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as benign.

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