7-117610521-G-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM1 BP4_Strong BS2

The NM_000492.4(CFTR):c.2991G>C(p.Leu997Phe) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00182 in 1,611,990 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L997L) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0021 (1 hom., cov: 31)
  • Exomes 𝑓: 0.0018 (8 hom.)
• Consequence: CFTR NM_000492.4 missense, splice_region
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:18 B:3 O:2
• Conservation: PhyloP100: 1.65

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]

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 9 uncertain in NM_000492.4
• BP4: Computational evidence support a benign effect (MetaRNN=0.02057156).
• BS2: High Homozygotes in GnomAdExome at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFTR	NM_000492.4	c.2991G>C	p.Leu997Phe	missense_variant, splice_region_variant	19/27	ENST00000003084.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFTR	ENST00000003084.11	c.2991G>C	p.Leu997Phe	missense_variant, splice_region_variant	19/27	1	NM_000492.4	P2
	ENST00000456270.1	n.178-5532C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.00211 AC: 320 AN: 151454 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.000437

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00658

Gnomad ASJ AF: 0.00577

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00125

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00321

Gnomad NFE AF: 0.00243

Gnomad OTH AF: 0.00482

GnomAD3 exomes AF: 0.00229 AC: 576 AN: 251082 Hom.: 3 AF XY: 0.00244 AC XY: 331 AN XY: 135692

Gnomad AFR exome AF: 0.000246

Gnomad AMR exome AF: 0.00420

Gnomad ASJ exome AF: 0.00536

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00141

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00260

Gnomad OTH exome AF: 0.00573

GnomAD4 exome AF: 0.00179 AC: 2617 AN: 1460462 Hom.: 8 Cov.: 31 AF XY: 0.00192 AC XY: 1398 AN XY: 726580

Gnomad4 AFR exome AF: 0.000359

Gnomad4 AMR exome AF: 0.00455

Gnomad4 ASJ exome AF: 0.00571

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00140

Gnomad4 FIN exome AF: 0.0000562

Gnomad4 NFE exome AF: 0.00169

Gnomad4 OTH exome AF: 0.00337

GnomAD4 genome AF: 0.00211 AC: 320 AN: 151528 Hom.: 1 Cov.: 31 AF XY: 0.00212 AC XY: 157 AN XY: 73992

Gnomad4 AFR AF: 0.000436

Gnomad4 AMR AF: 0.00657

Gnomad4 ASJ AF: 0.00577

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00125

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00243

Gnomad4 OTH AF: 0.00478

Alfa AF: 0.00235 Hom.: 1

Bravo AF: 0.00262

TwinsUK AF: 0.00270 AC: 10

ALSPAC AF: 0.00104 AC: 4

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00209 AC: 18

ExAC AF: 0.00209 AC: 254

Asia WGS AF: 0.000866 AC: 3 AN: 3478

EpiCase AF: 0.00360

EpiControl AF: 0.00492

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:6 Uncertain:18 Benign:3 Other:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:2 Uncertain:9

Uncertain significance, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 27, 2023	The CFTR c.2991G>C; p.Leu997Phe variant (rs1800111) has been identified in multiple individuals diagnosed with CFTR-related disorders (Bergougnoux 2015, Gallati 2009, Gomez-Lira 2000, Hamoir 2013, Lucarelli 2010, Masson 2013, Pelletier 2010), but case control studies disagree if this variant is enriched in pancreatitis patients (LaRusch 2014, Gomez-Lira 2000). In addition, individuals homozygous for this variant have been reported to be clinically asymptomatic (Derichs 2005, Stanke 2008, Terlizzi 2017). Functional characterization of the variant protein indicates a reduction in the CFTR chloride transport activity (Bergougnoux 2015, Sosnay 2013, Van Goor 2014), but at a level unlikely to cause cystic fibrosis (Sosnay 2013, Strom 2011). This variant is reported in ClinVar (Variation ID: 7229) and is observed in the general population at a frequency of 0.22% (627/282204 alleles, including 3 homozygotes) in the Genome Aggregation Database. The leucine at codon 997 is highly conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.625). Due to the conflicting information regarding this variant, its clinical significance cannot be determined with certainty. References: Bergougnoux A et al. Should diffuse bronchiectasis still be considered a CFTR-related disorder? J Cyst Fibros. 2015; 14(5):646-53. PMID: 25797027. Derichs N et al. Homozygosity for L997F in a child with normal clinical and chloride secretory phenotype provides evidence that this cystic fibrosis transmembrane conductance regulator mutation does not cause cystic fibrosis. Clin Genet. 2005; 67(6):529-31. PMID: 15857421. 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. Gomez-Lira M et al. High frequency of cystic fibrosis transmembrane regulator mutation L997F in patients with recurrent idiopathic pancreatitis and in newborns with hypertrypsinemia. Am J Hum Genet. 2000; 66(6):2013-4. PMID: 10801389. Hamoir C et al. Clinical and morphological characteristics of sporadic genetically determined pancreatitis as compared to idiopathic pancreatitis: higher risk of pancreatic cancer in CFTR variants. Digestion. 2013; 87(4):229-39. PMID: 23751316. 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. Lucarelli M et al. A new complex allele of the CFTR gene partially explains the variable phenotype of the L997F mutation. Genet Med. 2010; 12(9):548-55. PMID: 20706124. 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. Pelletier A et al. CFTR gene mutation in patients with apparently idiopathic pancreatitis: lack of phenotype-genotype correlation. Pancreatology. 2010; 10(2-3):158-64. PMID: 20460946. Sosnay PR et al. Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet. 2013; 45(10):1160-7. PMID: 23974870. Stanke F et al. Diversity of the basic defect of homozygous CFTR mutation genotypes in humans. J Med Genet. 2008; 45(1):47-54. PMID: 18178635. Strom C et al. The dangers of including nonclassical cystic fibrosis variants in population-based screening panels: p.L997F, further genotype/phenotype correlation data. Genet Med. 2011; 13(12):1042-4. PMID: 21804385. Terlizzi V et al. Genotype-phenotype correlation and functional studies in patients with cystic fibrosis bearing CFTR complex alleles. J Med Genet. 2017 Apr;54(4):224-235. PMID: 27738188. Van Goor F et al. Effect of ivacaftor on CFTR forms with missense mutations associated with defects in protein processing or func -
Uncertain significance, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 12, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2024	CFTR: PM3:Very Strong, PM2:Supporting, PS3:Supporting -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Dec 16, 2021	- -
Uncertain significance, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Dec 27, 2018	The L997F variant in the CFTR gene has been reported previously in trans with another pathogenic CFTR variant in individuals with cystic fibrosis and atypical cystic fibrosis, as well as in asymptomatic individuals (Lucarelli et al., 2010; Strom et al., 2011; Schippa et al., 2013). It has been suggested that the presence of the R117L variant in cis with L997F as a complex allele may in part explain the variable phenotype observed in individuals with the L997F variant (Lucarelli et al., 2010). The L997F variant is observed in 59/10,146 (0.58%) alleles from individuals of Ashkenazi Jewish background in large population cohorts (Lek et al., 2016). The L997F variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. Functional studies demonstrated that the L997F variant was associated with somewhat reduced chloride transport (VanGoor et al., 2014). We interpret L997F as a variant of uncertain significance. -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jul 31, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 02, 2023	The CFTR c.2991G>C (p.Leu997Phe) variant has been reported with other CFTR variants in the published literature in individuals with Cystic Fibrosis (CF) (PMID: 1379210 (1992), 9921909 (1998), 17572159 (2008), 20706124, 21804385 (2011), 23613805 (2013), 27738188 (2016)) and CF-related disorders including pancreatitis (PMID: 10801389 (2000), 18501000 (2008), 20460946 (2010), 23951356 (2013), 29589582 (2018)), bronchiectasis (PMID: 9921909 (1998)) and congenital bilateral absence of the vas deferens (CBAVD) (PMID: 9272157 (1997), 10875853 (2000), 26911355 (2016)). This variant is also found to occur as part of a complex allele p.[R117L; L997F] and is often associated with a more severe phenotype in individuals with cystic fibrosis (PMID: 25910067 (2015)). This variant has also been reported in asymptomatic individuals (PMID: 12014388 (2002), 15857421 (2005)). Functional studies indicated that this variant results in reduction of CFTR chloride transport activity, channel diameter and alters bicarbonate permeability (PMID: 25824995 (2015), 23891399 (2014), 25033378 (2014)). The frequency of this variant in the general population, 0.0099 (115/11590 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 predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant. -

Cystic fibrosis Pathogenic:1 Uncertain:5 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Pars Genome Lab	May 18, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Eurofins-Biomnis	Dec 01, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, The Hospital for Sick Children	Aug 14, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	Nov 05, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Mar 22, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Jan 30, 2024	The p.L997F variant (also known as c.2991G>C), located in coding exon 19 of the CFTR gene, results from a G to C substitution at nucleotide position 2991. The leucine at codon 997 is replaced by phenylalanine, an amino acid with highly similar properties. This alteration is known to occur in isolation or as part of a complex allele, p.[R117L;L997F], and it is associated with a range of clinical outcomes (Stanke F et al. J. Med. Genet., 2008 Jan;45:47-54; Lucarelli M et al. Genet Med, 2010 Sep;12:548-55; Strom CM et al. Genet Med, 2011 Dec;13:1042-4; Lucarelli M et al. Mol Med, 2015 Apr;21:257-75; Terlizzi V et al. J. Med. Genet., 2017 04;54:224-235). Some individuals homozygous for p.L997F or compound heterozygous with a second CFTR mutation were reported to be asymptomatic, whereas others had intermediate sweat chloride levels and exhibited CFTR-related disorders, including congenital bilateral absence of the vas deferens, pancreatitis, and bronchiectasis. In contrast, the p.[R117L;L997F] complex allele is associated with a more severe phenotype and has been described in multiple homozygous or compound heterozygous individuals with elevated sweat chloride level and cystic fibrosis. In functional studies, p.R117L was shown to retain normal CFTR maturation/processing, but result in approximately 20% of wild-type CFTR function (Sosnay PR et al. Nat Genet, 2013 Oct;45:1160-7; Van Goor F et al. J. Cyst. Fibros., 2014 Jan;13:29-36). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on available evidence to date, this variant is unlikely to be causative of classic cystic fibrosis when it occurs in isolation; however, its contribution to the development of a CFTR-related disorder is uncertain. This alteration is thus classified as a variant of unknown significance. -

CFTR-related disorder Pathogenic:2 Uncertain:2 Benign:1

Pathogenic, criteria provided, single submitter	curation	CFTR-France	Jan 29, 2018	- -
Likely benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Oct 27, 2022	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Uncertain significance, 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. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Likely pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, The Hospital for Sick Children	Aug 14, 2019	- -
Uncertain significance, no assertion criteria provided	clinical testing	Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals	Oct 29, 2021	- -

Obstructive azoospermia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Institute of Reproductive Genetics, University of Münster

Mar 16, 2022

- -

Pancreatitis Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital

Sep 15, 2015

- -

Infertility disorder Uncertain:1

Uncertain significance, no assertion criteria provided

provider interpretation

MAGI's Lab - Research, MAGI Group

-

- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

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

Nov 12, 2020

Variant summary: CFTR c.2991G>C (p.Leu997Phe) results in a non-conservative amino acid change located in the ABC transporter type 1, transmembrane domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0024 in 254424 control chromosomes in the gnomAD database, including 3 homozygotes. This frequency is not significantly higher than expected for a pathogenic variant in CFTR causing Cystic Fibrosis (0.0024 vs 0.013), allowing no conclusion about variant significance. c.2991G>C has been reported in the literature in patients with a wide range of atypical CFTR-related phenotypes such as bronchiectasis, pancreatitis, hypertrypsinemia, asthma, renal agenesis without a strong evidence of causality (example, Lebecque_2011, Tzetis_2001, Casals_2000, Padoan_2002); it is also found in ~ 1% of normal alleles from various studies. Of note, two homozygote individuals, one completely unaffected (Derichs_2005) and one only affected with allergic bronchopulmonary aspergillosis (ABPA) (Lebecque_2011) have been reported. The variant has also been found to be in cis with other CFTR deleterious variants such as deltaF508 (Fanen_1992), a large deletion spanning exons 2-9 of the CFTR gene (Schneider_2007, Strom_2011) and with R117L (Lucarelli_2010, classified as likely pathogenic) in CF patients supporting a benign outcome. Lastly, the variant has also been reported as having been co-inherited with a disease causing deletion spanning the entire SPINK1 gene in one family segregating with chronic pancreatitis (Masson_2007, cited in Bombieri_2011) supporting an alternative molecular basis of disease. These data indicate that the variant is unlikely to be associated with CF or any of its related variably expressive disease phenotypes. Reputed databases such as CFTR2 cite this variant as not disease causing (Sosnay_2013). In addition, functional studies suggest the variant could play a role in bicarbonate permeability relevant to organs in which CFTR is used for bicarbonate secretion (LaRush_2014) and has significantly reduced chloride conductance (Van Goor_2013), however the in vivo impact of these functional defects are unknown. Twelve clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments, at-least two other submitters report a benign/likely benign outcome. Based on the evidence outlined above, the variant in isolation was classified as benign for CF and associated phenotypes. -

Hypertrypsinemia, neonatal, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jan 01, 2001

- -

Pancreatitis, idiopathic, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jan 01, 2001

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.74
BayesDel_addAF	Benign	-0.067	T
BayesDel_noAF	Pathogenic	0.14
Cadd	Benign	22
Dann	Uncertain	1.0
DEOGEN2	Uncertain	0.59	D;.;.;T;.
Eigen	Uncertain	0.40
Eigen_PC	Uncertain	0.33
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Uncertain	0.96	D;D;D;D;D
M_CAP	Uncertain	0.12	D
MetaRNN	Benign	0.021	T;T;T;T;T
MetaSVM	Uncertain	0.21	D
MutationAssessor	Benign	1.8	L;.;.;.;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.59	T
PROVEAN	Benign	-1.0	N;.;.;N;.
REVEL	Uncertain	0.63
Sift	Benign	0.053	T;.;.;D;.
Sift4G	Pathogenic	0.0	D;.;.;D;.
Polyphen		1.0	D;.;.;.;.
Vest4		0.95
MutPred		0.73		Loss of stability (P = 0.2182);.;.;.;.;
MVP		1.0
MPC		0.0045
ClinPred		0.029	T
GERP RS		2.9
Varity_R		0.61
gMVP		0.93

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: rs1800111; hg19: chr7-117250575;