ClinVar Miner

Submissions for variant NM_000492.3(CFTR):c.2604A>G (p.Val868=) (rs1800105)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001007591 SCV000625738 likely benign Cystic fibrosis 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000781248 SCV000919156 benign not specified 2018-10-08 criteria provided, single submitter clinical testing Variant summary: CFTR c.2604A>G results in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing, which is further supported with a functional study (Scott_2012). The variant allele was found at a frequency of 1.2e-05 in 246264 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.2604A>G has been reported in the literature in individuals affected with Cystic Fibrosis (Pignatti_1996, Claustres_2017, Bombieri_1998, Devoto_1991), in whom a pathogenic CFTR variant in cis (c.3196C>T, p.Arg1066Cys) was reported (Pignatti_1996, Claustres_2017). Furthermore, a reputable database (CFTR - France) reports the variant to co-occur with pathogenic CFTR variant in 3 individuals, along with multiple internal testing specimens in whom two other confirmed pathogenic variants in the CFTR gene were identified (c.579+1G>T;c.3196C>T [1 internal case]and c.1521_1523delCTT;c.3196C>T [2 internal cases]), further supporting a benign role. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as likely benign. Based on the evidence outlined above, the variant was classified as benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000552909 SCV001134129 benign not provided 2019-04-16 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000781248 SCV001158185 benign not specified 2019-02-21 criteria provided, single submitter clinical testing
Johns Hopkins Genomics,Johns Hopkins University RCV001007591 SCV001167241 likely benign Cystic fibrosis 2019-10-14 criteria provided, single submitter clinical testing

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