rs142540482

Positions:

• chr7-117509090-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 6P and 2B. PM1 PM2 PM5 BP4_Moderate

The NM_000492.4(CFTR):​c.221G>A​(p.Arg74Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000534 in 1,612,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R74W) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00024 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00056 (0 hom.)
• Consequence: CFTR NM_000492.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:12 B:1
• Conservation: PhyloP100: 3.83

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 Uncertain_significance. Variant got 4 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 14 uncertain in NM_000492.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr7-117509090-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1706004.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP4: Computational evidence support a benign effect (MetaRNN=0.20756286).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFTR	NM_000492.4	c.221G>A	p.Arg74Gln	missense_variant	3/27	ENST00000003084.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFTR	ENST00000003084.11	c.221G>A	p.Arg74Gln	missense_variant	3/27	1	NM_000492.4	P2

Frequencies

GnomAD3 genomes AF: 0.000243 AC: 37 AN: 152116 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000965

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000456

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000263 AC: 66 AN: 250994 Hom.: 0 AF XY: 0.000236 AC XY: 32 AN XY: 135664

Gnomad AFR exome AF: 0.000123

Gnomad AMR exome AF: 0.0000579

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000109

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000529

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000565 AC: 825 AN: 1460682 Hom.: 0 Cov.: 29 AF XY: 0.000550 AC XY: 400 AN XY: 726748

Gnomad4 AFR exome AF: 0.0000598

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.0000376

Gnomad4 NFE exome AF: 0.000710

Gnomad4 OTH exome AF: 0.000431

GnomAD4 genome AF: 0.000243 AC: 37 AN: 152234 Hom.: 0 Cov.: 33 AF XY: 0.000202 AC XY: 15 AN XY: 74418

Gnomad4 AFR AF: 0.0000963

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000456

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000427 Hom.: 0

Bravo AF: 0.000280

TwinsUK AF: 0.000539 AC: 2

ALSPAC AF: 0.000259 AC: 1

ESP6500AA AF: 0.000454 AC: 2

ESP6500EA AF: 0.00105 AC: 9

ExAC AF: 0.000189 AC: 23

Asia WGS AF: 0.000289 AC: 1 AN: 3474

EpiCase AF: 0.000327

EpiControl AF: 0.000356

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:12 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Cystic fibrosis Uncertain:7

Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Oct 24, 2017	- -
Uncertain significance, criteria provided, single submitter	curation	Institute of Human Genetics, University of Leipzig Medical Center	Sep 05, 2022	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, BP2, BP4 -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	May 25, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Sep 08, 2022	The p.R74Q variant (also known as c.221G>A), located in coding exon 3 of the CFTR gene, results from a G to A substitution at nucleotide position 221. The arginine at codon 74 is replaced by glutamine, an amino acid with highly similar properties. This variant was reported in an individual with idiopathic chronic pancreatitis who was negative for mutations in the PRSS1 gene (Rosendahl J et al. Pancreatology, 2010 May;10:165-72). Functional studies found that this variant did not affect chloride current density, but significantly reduced bicarbonate permeability and conductance in HEK 293T cells, which may increase the risk of pancreatitis (LaRusch J et al. PLoS Genet., 2014 Jul;10:e1004376; Kim Y et al. Cell Mol Gastroenterol Hepatol, 2020 Sep;9:79-103). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on available evidence, this variant is unlikely to be causative of classic CF, however its clinical contribution to the development of a CFTR-related disorder is uncertain. -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Oct 04, 2022	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 74 of the CFTR protein (p.Arg74Gln). This variant is present in population databases (rs142540482, gnomAD 0.05%). This missense change has been observed in individual(s) with chronic pancreatitis (PMID: 17003641, 21520337, 22427236, 25033378). ClinVar contains an entry for this variant (Variation ID: 53456). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CFTR protein function. Experimental studies have shown that this missense change affects CFTR function (PMID: 31561038). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Johns Hopkins Genomics, Johns Hopkins University	Feb 13, 2023	Previously reported CFTR variant that has been identified in individuals with pancreatitis and has an entry in ClinVar (Variation ID: 53456). This CFTR variant (rs142540482) is rare (<0.1%) in a large population dataset (gnomADv2.1.1: 72/282380 total alleles; 0.0255%; no homozygotes). Functional studies have shown that this variant has a normal chloride current, but impaired conductance of and permeability to bicarbonate. The latter has been be associated with pancreatitis risk. The clinical significance of this variant is uncertain at this time. -

not provided Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 26, 2022	The CFTR c.221G>A; p.Arg74Gln variant (rs142540482) has been reported in multiple pancreatitis patients (Keiles 2006, Masson 2013, Rosendahl 2013, LaRusch 2014) but did not show significant enrichment in patients compared to unaffected individuals (Rosendahl 2013, LaRusch 2014). Functional studies indicate that the variant protein has a defect in bicarbonate transport, but has no impact on chloride transport activity (LaRusch 2014). This variant is reported in ClinVar (Variation ID: 53456) and is found in the non-Finnish European population with an overall allele frequency of 0.05% (64/128878 alleles) in the Genome Aggregation Database. The arginine at residue 74 is moderately conserved, and computational algorithms are uncertain whether this variant is neutral or deleterious (REVEL: 0.483). Due to the limited and conflicting information regarding this variant, its clinical significance cannot be determined with certainty. References: Keiles S et al. Identification of CFTR, PRSS1, and SPINK1 mutations in 381 patients with pancreatitis. Pancreas. 2006 33(3):221-7. PMID: 17003641 LaRusch J et al. Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis. PLoS Genet. 2014 10(7):e1004376. PMID: 25033378. 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. Rosendahl J et al. CFTR, SPINK1, CTRC and PRSS1 variants in chronic pancreatitis: is the role of mutated CFTR overestimated? 2013 Gut. 62(4):582-92. PMID: 22427236. -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 19, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	May 07, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 21, 2023	The CFTR c.221G>A (p.Arg74Gln) variant has been reported in the published literature in individuals affected with congenital absence of the vas deferens (PMID: 31845523 (2020), 21520337 (2011)), and pancreatitis (PMID: 17003641 (2006), 20460947 (2010), 21520337 (2011), 22427236 (2013)). Published functional studies show normal but reduced bicarbonate permeability and conductance (PMID: 25033378 (2014), PMID: 31561038 (2020)). The frequency of this variant in the general population, 0.00083 (42/50662 chromosomes (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. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Apr 27, 2023

Variant summary: CFTR c.221G>A (p.Arg74Gln) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. One publication (Ramalho_2015) and 2/4 computational tools predict that the variant creates a cryptic 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00026 in 254510 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in CFTR causing Chronic Pancreatitis Risk (0.00026 vs 0.0063), allowing no conclusion about variant significance. The variant was reported in one patient with a CFTR-related disorder (unspecified phenotype) however, this patient also carried a pathogenic CFTR variant (c.3846G>A, p.W1282X) in cis, supporting a benign role for the variant of interest in this case (Trujillano_2013). On the other hand, multiple publications cite the variant in individuals with pancreatitis (e.g. Keiles_2006, Steiner_2011, Rosendahl_2012, Masson_2013, LaRusch_2014). In several patients, the variant was reported along with p.R297Q (phase not specified), and this co-occurring variant (i.e. c.890G>A, p.Arg297Gln), was also reported in several patients with idiopathic pancreatitis. Additionally, the variant was found to be associated with pancreatitis in a case control study when patients also have the SPINK1 pathogenic mutation p.N34S (LaRusch_2014). This study also reported experimental evidence that the c.221G>A, p.Arg74Gln variant results in significantly reduced bicarbonate channel function (LaRusch_2014). Similarly, another functional study has reported that the variant impairs the association of CFTR with WNK1, reducing WNK1-mediated regulation of HCO3- channel activity (Kim_2019). Authors of the former study (LaRusch_2014) concluded that variants that impair bicarbonate permeation may increase the risk for pancreatitis, but not for cystic fibrosis. In contrast, a recent meta-analysis of CFTR variants characterized by a selective bicarbonate conductance defect did not find a significant association of p.Arg74Gln with chronic pancreatitis (Berke_2022). The following publications have been ascertained in the context of this evaluation (PMID: 36264955, 17003641, 34973142, 31561038, 25033378, 23951356, 29859674, 34782259, 22427236, 21520337, 23687349). Eleven submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and classfied the variant as either VUS (n=10) or likely benign (n=1). Based on the evidence outlined above, the variant was classified as VUS. -

CFTR-related disorder Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.082
BayesDel_addAF	Uncertain	0.13	D
BayesDel_noAF	Pathogenic	0.29
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.39	T;.;.;T;.
Eigen	Benign	0.033
Eigen_PC	Uncertain	0.22
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Uncertain	0.92	D;D;D;D;D
M_CAP	Pathogenic	0.34	D
MetaRNN	Benign	0.21	T;T;T;T;T
MetaSVM	Uncertain	-0.11	T
MutationAssessor	Uncertain	2.2	M;.;.;.;M
MutationTaster	Benign	0.55	D;N
PrimateAI	Benign	0.47	T
PROVEAN	Benign	-0.58	N;.;.;N;.
REVEL	Uncertain	0.48
Sift	Benign	0.41	T;.;.;T;.
Sift4G	Benign	0.13	T;.;.;T;.
Polyphen		0.0030	B;.;.;.;.
Vest4		0.74
MVP		0.95
MPC		0.0038
ClinPred		0.049	T
GERP RS		5.7
Varity_R		0.41
gMVP		0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs142540482; hg19: chr7-117149144;