This variant was identified in 1 patient with a clinically confirmed diagnosis of cystic fibrosis. The variant was classified in the context of a project re-classifying variants in the German Cystic Fibrosis Registry (Muko.e.V.). Link: https://www.muko.info/angebote/qualitaetsmanagement/register/cf-einrichtungen/mukoweb. Criteria applied: PS3_SUP, PM3, PM5, BS3, BS4, BP2

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

Published functional studies are inconclusive: reduced bicarbonate:chloride transport ratio with chloride channel function similar to or less than wildtype but not as severe as positive controls (PMID: 9305991, 11242048, 38388235); Identified in individuals with cystic fibrosis (CF) or CFTR-related disorders, including patients with pancreatitis (PMID: 11022925, 11288718, 11168024, 24418186, 17003641, 22094894, 20846557, 40065563); In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25087612, 18456578, 11288708, 9305991, 11288718, 11242048, 20416310, 20021716, 24418186, 23514810, 20846557, 22094894, 17003641, 16778595, 8818956, 23951356, 11354633, 11022925, 29589582, 11168024, 23523379, 1284534, 7551394, 15097853, 11788091, 34782259, 32508047, 34996830, 38695616, 38515211, 40044664, 38388235, 39855646, 40065563, 37628659, 40070865, Canbek2024[CaseReport], 8680407)

Variant summary: CFTR c.890G>A (p.Arg297Gln) results in a conservative amino acid change located in the first transmembrane domain (IPR011527), within the second cytoplasmic loop (Choi_2001) of the encoded protein sequence. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change. The variant allele was found at a frequency of 0.00056 in 251720 control chromosomes, predominantly at a frequency of 0.0011 within the Non-Finnish European subpopulation in the gnomAD database. This frequency is not significantly higher than estimated for disease-causing variants in CFTR, allowing no conclusion about variant significance. c.890G>A has been reported in the literature in multiple individuals affected with a milder, atypical form of cystic fibrosis (Graham_1991 [no PMID], Hughes_2001) and was detected in neonates with positive newborn screening sweat test results (Scotet_2000, Bozdogan_2021), however in Scotet_2000 the CFTR gene was not fully sequenced. The variant was also reported with various CFTR-related phenotypes, e.g. asthma (Tzetis_2001) infertility (Ravnik-Glavac_2001, Gallati_2009), and cholestasis (Wang_2020). However, multiple affected individuals were reported to carry another pathogenic CFTR variant (5T) in cis with the variant of interest (Graham 1991, Hughes 2001, Tzetis 2001), along with a family study indicating that the variant did not segregate with the disease (Dorval 1995). The variant was also reported in patients affected with chronic or recurrent pancreatitis (e.g. Casals_2004, Keiles_2006, Sutton_2010, Sultan_2012, Masson_2013, LaRusch_2014). However, some of these patients also carried the variant CFTR c.221G>A (p.Arg74Gln) (e.g. Keiles_2006, Masson_2013), and this co-occurring variant (i.e. R74Q) was also reported in several patients with chronic- or idiopathic pancreatitis. Therefore, these data do not allow clear conclusions about variant significance. Functional studies found that the variant resulted in a chloride channel function similar to the wild-type (Seibert 1997), or moderately decreased chloride channel conductance, i.e. ~64% relative to wild type (Bihler_2024). On the other hand, an earlier study reported a significantly reduced bicarbonate transport (Choi 2001). According to a later study, other variants that impair bicarbonate permeation may increase the risk for pancreatitis, but not for cystic fibrosis (LaRusch 2014). The following publications have been ascertained in the context of this evaluation (PMID: 24418186, 33572515, 15097853, 11242048, 8680407, 7551394, 20021716, 29589582, 11288718, 23514810, 17003641, 25033378, 23951356, 33946859, 20416310, 11788091, 31674704, 11168024, 11022925, 9305991, 11288708, 22094894, 16778595, 20846557, 8818956, 9691989, 11354633, 31450232, 38388235). ClinVar contains an entry for this variant (Variation ID: 54082). Based on the evidence outlined above, the variant was classified as likely benign.

p.Arg297Gln variant in exon 8 of CFTR: This variant is not expected to have clin ical significance because it has been identified in 2 unaffected individuals in trans with a pathogenic variant (Dorval 1995). This variant has also been report ed in ClinVar (Variation ID 54082) and has been identified in 0.1% (155/126020) of European chromosomes by the Genome Aggregation Database (gnomAD, http://gnoma d.broadinstitute.org; dbSNP rs143486492). Computational prediction tools and con servation analysis suggest that the p.Arg297Gln variant may not impact the prote in, though this information is not predictive enough to rule out pathogenicity. ACMG/AMP Criteria applied: BS2, BP4.

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

The CFTR c.890G>A; p.Arg297Gln variant (rs143486492) is reported in the literature in multiple individuals affected with cystic fibrosis or CFTR-related disorders (Abou Alaiwa 2014, Casals 2004, Gallati 2009, Keiles 2006, Masson 2013, Raraigh 2022, Scotet 2000, Sultan 2012, Sutton 2010). However, this variant has also been reported on the same chromosome as the 5T variant (Hughes 2001, Tzetis 2001), and did not segregate with disease in at least one family (Dorval 1995). This variant is reported in ClinVar (Variation ID: 54082), and is found in the non-Finnish European population with an allele frequency of 0.12% (153/128492 alleles) in the Genome Aggregation Database (v2.1.1). Computational analyses predict that this variant is deleterious (REVEL: 0.717). Functional analyses of the variant protein show normal chloride channel activity (Chen 2000, Seibert 1997), but a defect in bicarbonate transport (Choi 2001). Due to conflicting information, the clinical significance of the p.Arg297Gln variant is uncertain at this time. References: Abou Alaiwa MH et al. Neonates with cystic fibrosis have a reduced nasal liquid pH; a small pilot study. J Cyst Fibros. 2014 Jul;13(4):373-7. PMID: 24418186. Casals T et al. Different CFTR mutational spectrum in alcoholic and idiopathic chronic pancreatitis? Pancreas. 2004 28(4):374-9. PMID: 15097853. Chen EY et al. Cystic fibrosis transmembrane conductance regulator has an altered structure when its maturation is inhibited. Biochemistry. 2000 Apr 4;39(13):3797-803. PMID: 10736180. Choi JY et al. Aberrant CFTR-dependent HCO3- transport in mutations associated with cystic fibrosis. Nature. 2001 Mar 1;410(6824):94-7. PMID: 11242048. Dorval I et al. French CF family genotype analysis shows that the R297Q mutation is a rare polymorphism. Hum Mutat. 1995;6(4):334-5. PMID: 8680407. Gallati S et al. Cystic fibrosis transmembrane conductance regulator mutations in azoospermic and oligospermic men and their partners. Reprod Biomed Online. 2009 19(5):685-94. PMID: 20021716. Hughes D et al. Mutation and haplotype analysis of the CFTR gene in atypically mild cystic fibrosis patients from Northern Ireland. J Med Genet. 2001 Feb;38(2):136-9. PMID: 11288718. Keiles S et al. Identification of CFTR, PRSS1, and SPINK1 mutations in 381 patients with pancreatitis. Pancreas. 2006 33(3):221-7. PMID: 17003641. Masson E et al. A conservative assessment of the major genetic causes of idiopathic chronic pancreatitis: data from a comprehensive analysis of PRSS1, SPINK1, CTRC and CFTR genes in 253 young French patients. PLoS One. 2013 8(8):e73522. PMID: 23951356. Raraigh KS et al. Complete CFTR gene sequencing in 5,058 individuals with cystic fibrosis informs variant-specific treatment. J Cyst Fibros. 2022 May;21(3):463-470. PMID: 34782259. Scotet V et al. Neonatal screening for cystic fibrosis in Brittany, France: assessment of 10 years' experience and impact on prenatal diagnosis. Lancet. 2000 Sep 2;356(9232):789-94. PMID: 11022925. Seibert FS et al. Disease-associated mutations in cytoplasmic loops 1 and 2 of cystic fibrosis transmembrane conductance regulator impede processing or opening of the channel. Biochemistry. 1997 Sep 30;36(39):11966-74. PMID: 9305991. Sultan M et al. Genetic prevalence and characteristics in children with recurrent pancreatitis. J Pediatr Gastroenterol Nutr. 2012 54(5):645-50. PMID: 22094894. Sutton JM et al. Total pancreatectomy and islet cell autotransplantation as a means of treating patients with genetically linked pancreatitis. Surgery. 2010 Oct;148(4):676-85; discussion 685-6. PMID: 20846557.

The variant is observed at an extremely low frequency in the gnomAD v4.1.0 dataset (total allele frequency: 0.088%). Predicted Consequence/Location: Missense variant In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.72 (>=0.6, sensitivity 0.68 and specificity 0.92)]. A different missense change at the same codon (p.Arg297Trp) has been reported to be associated with CFTR-related disorder (PMID: 9272157). However the evidence of pathogenicity is insufficient at this time. The variant has been reported at least twice as benign with clinical assertions and evidence for the classification (ClinVar ID: VCV000054082). Therefore, this variant is classified as VUS according to the recommendation of ACMG/AMP guideline.

The CFTR c.890G>A (p.Arg297Gln) variant has been reported in individuals with cystic fibrosis (CF) (PMID: 34782259 (2021)), mild/atypical CF (Graham et. al., J Med Genet (1991) 28(8):571, and PMID: 11288718 (2001)), and CFTR-related disorders (PMID: 33946859 (2021), 28502372 (2017), 25033378 (2014), 23951356 (2013), 22094894 (2012), 17003641 (2006)). This variant has also been identified in reportedly unaffected individuals who carried a CF-causing mutation on the opposing chromosome (PMID: 29589582 (2018), 8680407 (1995)). Functional studies indicate this variant has neutral to partial effect on CFTR chloride conductance, and reduced bicarbonate transport (PMID: 38388235 (2024), 11242048 (2001), 9305991 (1997)). The frequency of this variant in the general population (Genome Aggregation Database, http://gnomad.broadinstitute.org) is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is deleterious or benign. Based on the available information, we are unable to determine the clinical significance of this variant.

CFTR: PM5:Supporting, BS1:Supporting, BS4