rs121909021

Variant names:

• chr7-117540276-C-T
• rs121909021
• NM_000492.4:c.1046C>T

Variant summary

Our verdict is Uncertain significance. The variant received 5 ACMG points: 5P and 0B. PM1 PM5 PP2

The NM_000492.4(CFTR):​c.1046C>T​(p.Ala349Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000292 in 1,613,674 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A349P) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.00014 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00031 (0 hom.)
• Consequence: CFTR NM_000492.4 missense
• Clinical Significance: Uncertain significance reviewed by expert panel P:4 U:14
• Conservation: PhyloP100: 7.43
• Publications: 21 publications found

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]

CFTR Gene-Disease associations (from GenCC):

• cystic fibrosis

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), Myriad Women’s Health, Orphanet
• congenital bilateral absence of vas deferens

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary chronic pancreatitis

  Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 5 ACMG points.

• PM1: In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 22 uncertain in NM_000492.4
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr7-117540275-G-C is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 618892.
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 197 curated pathogenic missense variants (we use a threshold of 10). The gene has 46 curated benign missense variants. Gene score misZ: -3.1397 (below the threshold of 3.09). Trascript score misZ: -1.0868 (below the threshold of 3.09). GenCC associations: The gene is linked to hereditary chronic pancreatitis, cystic fibrosis, congenital bilateral absence of vas deferens.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFTR	NM_000492.4	c.1046C>T	p.Ala349Val	missense_variant	Exon 8 of 27	ENST00000003084.11	NP_000483.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFTR	ENST00000003084.11	c.1046C>T	p.Ala349Val	missense_variant	Exon 8 of 27	1	NM_000492.4	ENSP00000003084.6

Frequencies

GnomAD3 genomes AF: 0.000138 AC: 21 AN: 152110 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

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: 0.000279

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000108 AC: 27 AN: 251102 AF XY: 0.000103

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000579

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000212

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000308 AC: 450 AN: 1461564 Hom.: 0 Cov.: 31 AF XY: 0.000261 AC XY: 190 AN XY: 727078

African (AFR) AF: 0.0000597 AC: 2 AN: 33476

American (AMR) AF: 0.0000447 AC: 2 AN: 44716

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26132

East Asian (EAS) AF: 0.00 AC: 0 AN: 39692

South Asian (SAS) AF: 0.00 AC: 0 AN: 86250

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53406

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.000374 AC: 416 AN: 1111748

Other (OTH) AF: 0.000497 AC: 30 AN: 60376

GnomAD4 genome AF: 0.000138 AC: 21 AN: 152110 Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12 AN XY: 74294

African (AFR) AF: 0.0000241 AC: 1 AN: 41422

American (AMR) AF: 0.0000655 AC: 1 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5200

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10600

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.000279 AC: 19 AN: 68006

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.000120 Hom.: 0

Bravo AF: 0.000155

TwinsUK AF: 0.000270 AC: 1

ALSPAC AF: 0.000519 AC: 2

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000465 AC: 4

ExAC AF: 0.000132 AC: 16

EpiCase AF: 0.000709

EpiControl AF: 0.000533

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:4 Uncertain:14

Revision: reviewed by expert panel

Submissions by phenotype

Cystic fibrosis Pathogenic:1 Uncertain:8

Dec 08, 2016

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Jul 22, 2021

Genome-Nilou Lab

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 22, 2020

Johns Hopkins Genomics, Johns Hopkins University

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CFTR variant of uncertain clinical significance. See www.CFTR2.org for phenotype information. -

Oct 03, 2017

CFTR2

Significance: Uncertain significance

Review Status: reviewed by expert panel

Collection Method: research

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Neuberg Centre For Genomic Medicine, NCGM

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CFTR c.1046C>T; p.Ala349Val variant has been reported in patients diagnosed with congenital bilateral absence of vas deferens (Dayangac 2004) or pancreatitis (Keiles 2006), when found in-trans with pathogenic CFTR variants (Dayangac 2004). Functional studies show this variant to have approximately 45% of wild type function (Raraigh 2018). The observed variant has been submitted to ClinVar with conflicting interpretation of pathogenicity (Pathogenic/Likely Pathogenic/ Variant of Uncertain Significance). The p.Ala349Val variant is reported with the allele frequency (0.01%) in the gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The amino acid Ala at position 349 is changed to a Val changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by PolyPhen2 and the residue is conserved across species. The amino acid change p.Ala349Val in CFTR is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. According to Cystic fibrosis mutation database, the effect of homozygous mutation on this disorder is uncertain, hence the variant has been classified as a Variant of Uncertain Significance (VUS). -

May 05, 2017

Counsyl

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com. -

Dec 05, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 349 of the CFTR protein (p.Ala349Val). This variant is present in population databases (rs121909021, gnomAD 0.02%). This missense change has been observed in individuals with CFTR-related diseases, including recurrent pancreatitis, cystic fibrosis (CF), CF-related metabolic syndrome, and congenital bilateral absence of the vas deferens (PMID: 15070876, 15638824, 17003641, 22094894, 25754095, 26671754). ClinVar contains an entry for this variant (Variation ID: 7172). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt CFTR protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects CFTR function (PMID: 30046002). 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. -

May 31, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.A349V variant (also known as c.1046C>T), located in coding exon 8 of the CFTR gene, results from a C to T substitution at nucleotide position 1046. The alanine at codon 349 is replaced by valine, an amino acid with similar properties. This variant was identified in one individual with congenital bilateral absence of the vas deferens (CBAVD) and one individual with recurrent acute pancreatitis; both individuals were also heterozygous for a pathogenic mutation, but the phase is unknown (Dayangaç D et al. Hum. Reprod., 2004 May;19:1094-100; Sultan M et al. J. Pediatr. Gastroenterol. Nutr., 2012 May;54:645-50). In CFBE cells, this variant demonstrated 45% of wild type CFTR function (Raraigh KS et al. Am. J. Hum. Genet., 2018 Jun;102:1062-1077). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on available evidence to date, the clinical significance of this alteration remains unclear. -

Sep 21, 2022

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: research

- -

not provided Pathogenic:1 Uncertain:4

Sep 11, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CFTR c.1046C>T (p.Ala349Val) variant has been reported in the published literature in individuals with pancreatic sufficient cystic fibrosis (PMID: 25754095 (2015)), pancreatitis (PMID: 17003641 (2006), 22094894 (2012)), congenital bilateral absence of the vas deferens (CBAVD) (PMID: 8627844 (1996), 15070876 (2004)), and CFTR-related metabolic syndrome (CRMS) (PMID: 26671754 (2016)). A functional assay found this variant showed decreased CFTR function compared to wild-type (PMID: 29805046 (2018)). The frequency of this variant in the general population, 0.00022 (28/128882 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. -

Aug 24, 2017

Eurofins Ntd Llc (ga)

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 29, 2022

Mayo Clinic Laboratories, Mayo Clinic

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 08, 2023

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CFTR c.1046C>T; p.Ala349Val variant (rs121909021) has been reported in patients diagnosed with congenital bilateral absence of vas deferens (Dayangac 2004, Havasi 2010) or pancreatitis (Keiles 2006, Sultan 2010), when found in-trans with pathogenic CFTR variants (Dayangac 2004, Sultan 2012). Functional studies show this variant to have approximately 45% of wild type function (Raraigh 2018). This variant is reported in ClinVar (Variation ID: 7172). It is found in the general population with an overall allele frequency of 0.01% (32/282468 alleles) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.632). Due to its reported occurrence in CFTR-related disorders, the p.Ala349Val variant is classified as mildly pathogenic. References: Dayangac D et al. Mutations of the CFTR gene in Turkish patients with congenital bilateral absence of the vas deferens. Hum Reprod. 2004 May;19(5):1094-100. PMID: 15070876. Havasi V et al. Association of cystic fibrosis genetic modifiers with congenital bilateral absence of the vas deferens. Fertil Steril. 2010 Nov;94(6):2122-7. PMID: 20100616. Keiles S et al. Identification of CFTR, PRSS1, and SPINK1 mutations in 381 patients with pancreatitis. Pancreas. 2006 Oct;33(3):221-7. PMID: 17003641. Sultan M et al. Genetic prevalence and characteristics in children with recurrent pancreatitis. J Pediatr Gastroenterol Nutr. 2012 May;54(5):645-50. PMID: 22094894. Raraigh KS et al. Functional Assays Are Essential for Interpretation of Missense Variants Associated with Variable Expressivity. Am J Hum Genet. 2018 Jun 7;102(6):1062-1077. PMID: 29805046. -

Jul 01, 2024

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 34405919, 8627844, 11933191, 16635477, 15024729, 19324992, 25304080, 25735457, 33500538, 30046002, 7683952, 17003641, 31036917, 25087612, 26671754, 23523379, 25754095, 11168024, 15070876, 15638824, 20100616, 22094894, 29669919, 30888834, 33922413, 19897426, 34996830, 35652053, 36253274, 37873426, 29805046) -

Cystic fibrosis;C0403814:Congenital bilateral aplasia of vas deferens from CFTR mutation Pathogenic:1

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Baylor Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary pancreatitis Pathogenic:1

Mar 20, 2025

Mendelics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

VarIant NM_000492.4(CFTR):c.1046C>T (p.Ala349Val) has GnomAD 4.1 frequency of 0.0002919 with 0 homozygote. Reported as likely pathogenic in PMID 29805046 -

not specified Uncertain:1

Apr 28, 2025

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

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: CFTR c.1046C>T (p.Ala349Val) results in a non-conservative amino acid change located in the ABC transporter transmembrane region of the encoded protein sequence. Four of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00011 in 251726 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in CFTR causing Non-Classic Cystic Fibrosis (0.00011 vs 0.013), allowing no conclusion about variant significance. c.1046C>T has been reported in the literature as a non-informative genotype in individuals ranging from a healthy carrier male, CBAVD, laboratory based CF genotyping cohorts, pancreatitis, pancreatically sufficient CF and cystic fibrosis transmembrane regulator-related metabolic syndrome with normal sweat chloride levels (example, Audrezet_1993, Schlegel_1996, Scotet_2001, Ravnik-Glavac_2002, Castaldo_2005, Lucarelli_2006, Sultan_2012, Wooldridge_2015, Schwartz_2009, Havasi_2010, Keiles_2006, Levy_2016, Tamura_2018, McCague_2019). In our conservative assessment, these data do not allow any conclusion about variant significance. Three publications reporting experimental evidence evaluating an impact on protein function were ascertained in the context of this evaluation. The most pronounced variant effect results in 30%-50% of normal CFTR activity with a categorization as indeterminate (Raraigh_2018, Han_2018) and in approximately 38% of normal chloride channel conductance relative to wild type (Bihler_2024). The following publications have been ascertained in the context of this evaluation (PMID: 11168024, 17003641, 15638824, 19324992, 11933191, 7683952, 16635477, 8627844, 22094894, 20100616, 25735457, 25754095, 29805046, 30046002, 29669919, 26671754, 30888834, 38388235). ClinVar contains an entry for this variant (Variation ID: 7172). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

Bronchiectasis with or without elevated sweat chloride 1 Uncertain:1

Jan 26, 2023

Baylor Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.26
BayesDel_addAF	Uncertain	0.10	D
BayesDel_noAF	Pathogenic	0.20
CADD	Pathogenic	27
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.50	D;.;.;T;.
Eigen	Uncertain	0.40
Eigen_PC	Uncertain	0.51
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.98	D;D;D;D;D
M_CAP	Uncertain	0.22	D
MetaRNN	Uncertain	0.56	D;D;D;D;D
MetaSVM	Uncertain	0.33	D
MutationAssessor	Benign	0.20	N;.;.;.;N
PhyloP100		7.4
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	-0.23	N;.;.;N;.
REVEL	Uncertain	0.63
Sift	Benign	0.17	T;.;.;T;.
Sift4G	Uncertain	0.0030	D;.;.;D;.
Polyphen		0.91	P;.;.;.;.
Vest4		0.49
MVP		1.0
MPC		0.0064
ClinPred		0.54	D
GERP RS		5.3
Varity_R		0.42
gMVP		0.81
Mutation Taster		=18/82	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs121909021; hg19: chr7-117180330;