ClinVar Miner

Submissions for variant NM_000492.3(CFTR):c.2490+2T>C (rs1057516216)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000411517 SCV000485278 likely pathogenic Cystic fibrosis 2016-02-19 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000411517 SCV001363801 likely pathogenic Cystic fibrosis 2019-11-05 criteria provided, single submitter clinical testing Variant summary: CFTR c.2490+2T>C is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5' splicing donor site. Three predict the variant strengthens an alternate cryptic intronic 5' donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 188996 control chromosomes. To our knowledge, no occurrence of c.2490+2T>C in individuals affected with Cystic Fibrosis and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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