rs397508414

Positions:

• chr7-117602865-T-TA

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2 PP3_Moderate PP5_Strong

The NM_000492.4(CFTR):​c.2657+2_2657+3insA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000173 in 1,611,840 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★★).

• Frequency:
  • Genomes: 𝑓 0.000085 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00018 (0 hom.)
• Consequence: CFTR NM_000492.4 splice_region, intron
• Clinical Significance: Uncertain significance reviewed by expert panel P:11 U:4
• Conservation: PhyloP100: 1.82

Genes affected

CFTR (HGNC:1884): (CF transmembrane conductance regulator) This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. The encoded protein functions as a chloride channel, making it unique among members of this protein family, and controls ion and water secretion and absorption in epithelial tissues. Channel activation is mediated by cycles of regulatory domain phosphorylation, ATP-binding by the nucleotide-binding domains, and ATP hydrolysis. Mutations in this gene cause cystic fibrosis, the most common lethal genetic disorder in populations of Northern European descent. The most frequently occurring mutation in cystic fibrosis, DeltaF508, results in impaired folding and trafficking of the encoded protein. Multiple pseudogenes have been identified in the human genome. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 7-117602865-T-TA is Pathogenic according to our data. Variant chr7-117602865-T-TA is described in ClinVar as [Uncertain_significance]. Clinvar id is 53536.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=6, Uncertain_significance=4, Pathogenic=4}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFTR	NM_000492.4	c.2657+2_2657+3insA		splice_region_variant, intron_variant		ENST00000003084.11	NP_000483.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFTR	ENST00000003084.11	c.2657+2_2657+3insA		splice_region_variant, intron_variant		1	NM_000492.4	ENSP00000003084	P2

Frequencies

GnomAD3 genomes AF: 0.0000854 AC: 13 AN: 152206 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000557 AC: 14 AN: 251468 Hom.: 0 AF XY: 0.0000589 AC XY: 8 AN XY: 135908

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000123

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000182 AC: 266 AN: 1459634 Hom.: 0 Cov.: 30 AF XY: 0.000179 AC XY: 130 AN XY: 726290

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000233

Gnomad4 OTH exome AF: 0.000116

GnomAD4 genome AF: 0.0000854 AC: 13 AN: 152206 Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2 AN XY: 74362

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000162

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000162 Hom.: 0

Bravo AF: 0.000106

EpiCase AF: 0.000273

EpiControl AF: 0.0000593

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:11 Uncertain:4

Revision: reviewed by expert panel

Submissions by phenotype

Cystic fibrosis Pathogenic:4 Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	Nov 05, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Johns Hopkins Genomics, Johns Hopkins University	Oct 15, 2019	CFTR sequence variant of uncertain clinical significance (previously reported for this patient by mass spectrometry genotyping). See www.CFTR2.org for phenotype information. -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Jul 02, 2021	- -
Uncertain significance, reviewed by expert panel	research	CFTR2	Apr 10, 2012	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 15, 2016	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 21, 2024	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jun 30, 2023	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. -

not provided Pathogenic:5 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Oct 04, 2022	PM2, PM3_strong -
Likely pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Mar 21, 2023	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 15, 2017	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 08, 2023	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 23, 2024	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) -

CFTR-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

curation

CFTR-France

Jan 29, 2018

- -

Bronchiectasis with or without elevated sweat chloride 1 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Mar 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.94		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.94		Position offset: -2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs397508414; hg19: chr7-117242919;