ClinVar Miner

Submissions for variant NM_000492.3(CFTR):c.869+3A>C (rs1554380828)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Integrated Genetics/Laboratory Corporation of America RCV000590696 SCV000697051 uncertain significance not provided 2016-03-29 criteria provided, single submitter clinical testing Variant summary: The c.689+3A>C variant in CFTR gene is an intronic change that alters a conserved nucleotide. 5/5 in silico tools via Alamut predict this variant to affect a normal splicing pattern, however, these predictions have yet to be confirmed by in vitro/in vivo functional studies. Another variant at this position, c.689+3A>T, that was identified in CF pt and pt, presented with hypochloraemic alkalosis, displayed similar in silico pattern and was shown to lead to alternative splicing and complete skipping of exon 7. The variant of interest has not, to our knowledge, been reported in the affected individuals, nor has it been cited by reputable clinical laboratories/diagnostic centers, however was identified in one affected individual in whom presence of F508del was also confirmed. The variant is absent from the large control population dataset of ExAC (0/~114434 chromosomes). Taken together, the variant was classified as VUS-possibly pathogenic and reported by Integrated Genetics as "likely clinically significant" until new information becomes available.

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