ClinVar Genomic variation as it relates to human health

Variant summary: CFTR c.1585-2A>T 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: Three predict the variant creates/or strengthens a cryptic 5 donor site. Four predict the variant abolishes a 3 acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 250846 control chromosomes (gnomAD). c.1585-2A>T has been reported in the literature in an individual undergoing carrier screening (Beauchamp _2019). This report however, does not provide unequivocal conclusions about association of the variant with Cystic Fibrosis. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Another nucleotide change in the same location (c.1585-2A>G) has been reported as pathogenic in our internal database and in ClinVar. 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 likely pathogenic.

The splice site c.1585-2A>T variant in CFTR gene has been reported in ClinVar as Likely Pathogenic. The c.1585-2A>T variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic.

This sequence change affects an acceptor splice site in intron 11 of the CFTR gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CFTR are known to be pathogenic (PMID: 1695717, 7691345, 9725922). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with cystic fibrosis (PMID: 11788090). ClinVar contains an entry for this variant (Variation ID: 1027585). Studies have shown that disruption of this splice site alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 25066652). For these reasons, this variant has been classified as Pathogenic.

The c.1585-2A>T intronic variant results from an A to T substitution two nucleotides upstream from coding exon 12 in the CFTR gene. Alterations that disrupt the canonical splice site are expected to result in aberrant splicing. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and may result in the creation or strengthening of a novel splice acceptor site. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNAdecay; however, based on available data in the literature, the in-frame transcript is unlikely to occur. In one minigene expression assay, 5 different variants were tested at this acceptor site, and none of them resulted in the in-frame transcript (Sharma N. et al. Hum Mutat 2014 Oct;35(10):1249-59). Another study found that a different alteration at this position, c.1585-2A>G, resulted in skipping of exon 12 and retention of 6 nucleotides in intron 11 (both out-of-frame transcripts). The presence of these two transcripts was confirmed in total RNA obtained from a patient with c.1585-2A>G (Silva IAL et al. Biochim Biophys Acta Mol Basis Dis 2020 11;1866(11):165905). In the same minigene assay, a common mutation c.1585-1G>A (1717-1G>A), resulted in skipping of exon 12 and a deletion of 1 nucleotide in exon 12. Further, analysis of RNA from nasal epithelial cells revealed that c.1585-1G>A resulted in skipping of exon 12 in 3 patients (Hull J. et al. Hum Mol Genet 1993 Jun;2(6):689-92). The c.1585-2A>T variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD).This nucleotide position is highly conserved in available vertebrate species. Based on the majority of available evidence to date, this variant is likely to be pathogenic.