Submissions for variant NM_000492.4(CFTR):c.2657+2_2657+3insA

gnomAD frequency: 0.00009  dbSNP: rs397508414

Total submissions: 15

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
CFTR2	RCV000046646	SCV001981588	uncertain significance	Cystic fibrosis	2012-04-10	reviewed by expert panel	research
Labcorp Genetics (formerly Invitae), Labcorp	RCV000046646	SCV000074659	pathogenic	Cystic fibrosis	2024-01-21	criteria provided, single submitter	clinical testing	This sequence change falls in intron 16 of the CFTR gene. It does not directly change the encoded amino acid sequence of the CFTR protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs397508414, gnomAD 0.01%). This variant has been observed in individual(s) with cystic fibrosis, atypical/non-classic CF and/or borderline sweat chloride (PMID: 11101688, 12167682, 16189704, 18195584, 23974870, 24586523; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as c.2789+2insA. ClinVar contains an entry for this variant (Variation ID: 53536). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant does not affect mRNA splicing (PMID: 23974870, 25066652). For these reasons, this variant has been classified as Pathogenic.
Eurofins Ntd Llc (ga)	RCV000790809	SCV000226434	pathogenic	not provided	2017-05-15	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000046646	SCV000696914	likely pathogenic	Cystic fibrosis	2016-12-15	criteria provided, single submitter	clinical testing	Variant summary: The CFTR c.2657+2_2657+3insA variant, alternatively also known as 2789+2insA, is an intronic variant causing insertion of adenine in intron 16 in proximity of the splice donor site. Mutation Taster predicts a damaging outcome for this variant. In addition, 4/5 splice prediction tools predict abrogation of utilization of the splice donor site. Two independent functional studies by minigene assay show that this variant only causes intermediate skipping of exon (i.e. partial exon skipping) (Sosnay_2013, Sharma_2014). Relative amount of properly spliced RNA transcript and fully process protein generated by CFTR minigenes transfected into two human cell lines (HEK and CFBE41o-) were 717.3% and 808.3%, respectively (Sosnay_2013). The exon 16 (residues 874-886) encodes part of ABC transporter transmembrane region and thus its skipping is expected to be deleterious for protein function. In literature, this variant is widely reported as a pathogenic variant and is reported to cause non-classic CF with consistent genotype-phenotype data. In Caucasian CF population in US the variants allele frequency was 0.1% (Schrijver_2016). This variant was found in 2/121402 control chromosomes from ExAC, only observed in the European (Non-Finnish) subpopulation at a frequency of 0.003% (2/66738). Thus, this variant is clearly overrepresented in patient population in comparison to controls in population of European origin, strongly supporting for pathogenicity. One clinical laboratory has classified this variant as pathogenic. Considering all evidences, this variant is currently classified as likely pathogenic.
Mendelics	RCV000046646	SCV000886400	uncertain significance	Cystic fibrosis	2018-11-05	criteria provided, single submitter	clinical testing
Johns Hopkins Genomics, Johns Hopkins University	RCV000046646	SCV000992328	uncertain significance	Cystic fibrosis	2019-10-15	criteria provided, single submitter	clinical testing	CFTR sequence variant of uncertain clinical significance (previously reported for this patient by mass spectrometry genotyping). See www.CFTR2.org for phenotype information.
CFTR-France	RCV001009498	SCV001169593	pathogenic	CFTR-related disorder	2018-01-29	criteria provided, single submitter	curation
GeneDx	RCV000790809	SCV001791976	likely pathogenic	not provided	2024-09-23	criteria provided, single submitter	clinical testing	Published functional studies are inconclusive: minimal effect on CFTR splicing with generation of correctly spliced CFTR transcript close to wild type levels in two different cell lines; CFTR protein levels comparable to wild type (PMID: 23974870, 25066652); Classified as a variant of varying clinical consequence in a well-curated database (CFTR2); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 20144563, 12167682, 12000363, 31420175, 33957545, 31036917, 26014425, 23974870, 25066652, 11101688, 16189704, 27214204, 24586523, 15754262, 31611131, 33085659, 26708955, 23168765, 18195584, 36207272, 35623009, 34782259, 37867076)
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000790809	SCV002046467	uncertain significance	not provided	2023-08-08	criteria provided, single submitter	clinical testing	The CFTR c.2657+2_2657+3insA variant has been reported in the published literature in combination with another CFTR variant in individuals affected with cystic fibrosis as well as atypical/non-classic cystic fibrosis (PMIDs: 11101688 (2000), 12167682 (2002), 15754262 (2005), 16189704 (2005), 17283574 (2007), 20031113 (2010), 23974870 (2013), 24586523 (2014), and 27837951 (2016)). In addition, functional studies report this variant does not affect CFTR mRNA splicing and retains residual CFTR function (PMIDs: 23974870 (2013), 25066652 (2014), and 33085659 (2020)). The frequency of this variant in the general population, 0.00024 (12/50808 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Based on the available information, we are unable to determine the clinical significance of this variant.
Genetics and Molecular Pathology, SA Pathology	RCV000046646	SCV002556893	pathogenic	Cystic fibrosis	2021-07-02	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000046646	SCV002743785	likely pathogenic	Cystic fibrosis	2023-06-30	criteria provided, single submitter	clinical testing	The c.2657+2_2657+3insA intronic variant, results from an insertion of one nucleotide (A) after position 2657+2, two bases downstream of coding exon 16 of the CFTR gene. This variant has been detected in conjunction with a pathogenic mutation in CFTR by our laboratory. This variant was identified in an individual with cystic fibrosis who had a pathogenic mutation in trans (Zitkiewicz E et al. PLoS ONE, 2014 Feb;9:e89094). This alteration was also reported in two individuals with elevated sweat chloride levels and a second pathogenic CFTR mutation; however, phase was not determined (McGinniss MJ et al. Hum. Genet., 2005 Dec;118:331-8). In addition, this alteration was observed in two males with obstructive azoospermia, borderline sweat chloride levels, and p.F508del; however, phase was not determined (Jézéquel P et al. Mol. Hum. Reprod., 2000 Dec;6:1063-7; Davé S et al. Am. J. Kidney Dis., 2005 Mar;45:e41-4). One in vitro minigene study showed that this variant produces predominantly normal, but also some aberrantly spliced isoforms (Sharma N et al. Hum. Mutat., 2014 Oct;35:1249-59). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the majority of available evidence to date, this variant is likely to be pathogenic.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000790809	SCV003799480	likely pathogenic	not provided	2023-03-21	criteria provided, single submitter	clinical testing	The CFTR c.2657+2_2657+3insA variant (rs397508414), also known as 2789+2insA, has been described in the literature in individuals with mild and atypical cystic fibrosis such as congenital bilateral absence of the vas deferens (CBAVD) when in combination with a severe pathogenic variant on the opposite chromosome (Jezequel 2000, McGinniss 2005, Sosnay 2013, CFTR2 database). Additionally, in testing performed at ARUP Laboratories, this variant has been identified in individuals with pancreatitis or CBAVD that also carried additional CFTR pathogenic variants. The c.2657+2_2657+3insA variant is reported in ClinVar (Variation ID: 53536) and is found in the non-Finnish European population at an overall frequency of 0.01% (17/129184 alleles) in the Genome Aggregation Database. This variant inserts a single nucleotide within a conserved splice donor sequence, and computational analyses (Alamut v.2.11) predict that this variant may impact splicing by weakening the canonical donor splice site. However, in vitro functional studies demonstrate residual transcript and protein function (Joynt 2020, Sharma 2014), although it is uncertain if these assays reflect the expression of this variant from its native locus. Given its incidence in affected individuals who harbor a second severe pathogenic CFTR variant, the c.2657+2_2657+3insA variant is considered likely pathogenic for CFTR-related disorders. References: CFTR2 database: https://cftr2.org/ Jezequel P et al. Molecular screening of the CFTR gene in men with anomalies of the vas deferens: identification of three novel mutations. Mol Hum Reprod. 2000 Dec; 6(12):1063-7. PMID: 11101688. Joynt AT et al. Evaluation of both exonic and intronic variants for effects on RNA splicing allows for accurate assessment of the effectiveness of precision therapies. PLoS Genet. 2020 Oct 21;16(10):e1009100. PMID: 33085659. McGinniss MJ et al. Extensive sequencing of the CFTR gene: lessons learned from the first 157 patient samples. Hum Genet. 2005; 118(3-4):331-8. PMID: 16189704. Sharma N et al. Experimental assessment of splicing variants using expression minigenes and comparison with in silico predictions. Hum Mutat. 2014 Oct;35(10):1249-59. PMID: 25066652. Sosnay PR et al. Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet. 2013 Oct;45(10):1160-7. PMID: 23974870.
Mayo Clinic Laboratories, Mayo Clinic	RCV000790809	SCV003853543	likely pathogenic	not provided	2022-10-04	criteria provided, single submitter	clinical testing	PM2, PM3_strong
Baylor Genetics	RCV003473491	SCV004213320	likely pathogenic	Bronchiectasis with or without elevated sweat chloride 1	2024-03-01	criteria provided, single submitter	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000790809	SCV001549042	likely pathogenic	not provided		no assertion criteria provided	clinical testing	The CFTR c.2657+2insA variant was identified in multiple cases of cystic fibrosis as well as a obstructive ozoospermia case; in most cases the variant was found as a compound heterozygous variant with the deltaF508Del variant (Zietkiewicz_2014_PMID:24586523, Giacobbe_2012_PMID:23168765; Jezequel_2000_PMID:11101688; Visich_2002_PMID:12000363). The variant was identified in dbSNP (ID: rs397508414), ClinVar (classified as pathogenic by EGL Diagnostics, as likely pathogenic by Integrated Genetics and Invitae, and as uncertain significance by John Hopkins Genomics and Mendelics). The variant was identified in control databases in 18 of 282868 chromosomes at a frequency of 0.00006363 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 17 of 129184 chromosomes (freq: 0.000132) and African in 1 of 24964 chromosomes (freq: 0.00004), but was not observed in the Latino, Ashkenazi Jewish, East Asian, European (Finnish), Other, or South Asian populations. The c.2657+2insA variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict the loss of the canonical 5' splice site. However, functional analysis of this variant using minigene assays revealed minimal effects on splicing (Sharma_2014_PMID:25066652; Sosnay_2013_PMID:23974870). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic.