rs143860237

chr7-117542062-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_000492.4(CFTR):c.1163C>T(p.Thr388Met) variant causes a missense change. The variant allele was found at a frequency of 0.000115 in 1,602,538 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 Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T388K) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00011 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00012 (0 hom.)
• Consequence: CFTR NM_000492.4 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:13
• Conservation: PhyloP100: 4.06

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 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2851867).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFTR	NM_000492.4	c.1163C>T	p.Thr388Met	missense_variant	9/27	ENST00000003084.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFTR	ENST00000003084.11	c.1163C>T	p.Thr388Met	missense_variant	9/27	1	NM_000492.4	P2

Frequencies

GnomAD3 genomes AF: 0.000112 AC: 17 AN: 152118 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000163 AC: 41 AN: 250946 Hom.: 0 AF XY: 0.000199 AC XY: 27 AN XY: 135666

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000145

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000360

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000185

Gnomad OTH exome AF: 0.000654

GnomAD4 exome AF: 0.000116 AC: 168 AN: 1450420 Hom.: 0 Cov.: 26 AF XY: 0.000148 AC XY: 107 AN XY: 722566

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000112

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000126

Gnomad4 SAS exome AF: 0.000547

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000808

Gnomad4 OTH exome AF: 0.000150

GnomAD4 genome AF: 0.000112 AC: 17 AN: 152118 Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9 AN XY: 74284

Gnomad4 AFR AF: 0.0000724

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000149 Hom.: 1

Bravo AF: 0.0000793

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.000132 AC: 16

EpiCase AF: 0.000327

EpiControl AF: 0.000178

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:13

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Cystic fibrosis Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Sep 21, 2021	The p.T388M variant (also known as c.1163C>T), located in coding exon 9 of the CFTR gene, results from a C to T substitution at nucleotide position 1163. The threonine at codon 388 is replaced by methionine, an amino acid with similar properties. This variant was first reported in an individual with cystic fibrosis (CF) and pancreatic insufficiency (Zielenski J et al. Cystic Fibrosis Mutation Database [database online] Toronto, ON, Canada: SickKids; 5-23-96); however, a second CFTR alteration was not identified. This variant was also reported in one individual with asthma, normal sweat chloride levels, and no classic symptoms of CF (Tzetis M et al. Hum. Genet. 2001 Mar; 108(3):216-21). In addition, this variant has been seen in one individual with a clinical diagnosis of congenital bilateral absence of the vas deferens (CBAVD) who did not have a second CFTR alteration (Dayangaç D et al. Hum. Reprod. 2004 May; 19(5):1094-100). This amino acid position is well conserved in available vertebrate species; however, methionine is the reference amino acid in other 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Sep 05, 2022	This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 388 of the CFTR protein (p.Thr388Met). This variant is present in population databases (rs143860237, gnomAD 0.04%). This missense change has been observed in individual(s) with cystic fibrosis, congenital bilateral absence of the vas deferens, or asthma (PMID: 11354633, 15070876, 26708955). This variant is also known as c.1295C>T. ClinVar contains an entry for this variant (Variation ID: 495887). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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	Genome-Nilou Lab	May 18, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	Jun 19, 2023	- -

CFTR-related disorder Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 28, 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Nov 29, 2023	The CFTR c.1163C>T variant is predicted to result in the amino acid substitution p.Thr388Met. In the heterozygous state, this variant has been reported in a patient with asthma or COPD (Tzetis et al. 2001. PubMed ID: 11354633; Table S1, Saferali et al. 2022. PubMed ID: 34996830), and has also been reported in a patient with congenital bilateral absence of the vas deferens (CBAVD) (Dayangaç et al. 2004. PubMed ID: 15070876). This variant is reported in 0.036% of alleles in individuals of South Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Jun 08, 2018	- -

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 11, 2021	Variant summary: CFTR c.1163C>T (p.Thr388Met) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00016 in 250946 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in CFTR causing CFTR-Related Diseases (0.00016 vs 0.013), allowing no conclusion about variant significance. c.1163C>T has been reported in the literature in individuals affected with CFTR-Related Diseases including CF, CBAVD/CUAVD, asthma, and in children with positive newborn screening, without strong evidence for causality (Schrijver_2016, Dayangac_2004, Akinsal_2018, Tzetis_2001, Bozdogan_2021). These reports do not provide unequivocal conclusions about association of the variant with CFTR-Related Diseases. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Eight classify the variant as VUS while one classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital	Feb 02, 2020	- -

not provided Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Dec 17, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 25, 2017	- -

Hereditary pancreatitis Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Aug 23, 2021

The CFTR c.1163C>T; p.Thr388Met variant (rs143860237) is reported in the literature in an individual with asthma (Tzetis 2001) and an individual with congenital bilateral absence of the vas deferens (Dayangac 2004). It is reported in ClinVar (Variation ID: 495887), and is observed in the general population at an overall frequency of 0.015% (43/282316 alleles) in the Genome Aggregation Database. The threonine at codon 388 is moderately conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.601). Due to limited information, the clinical significance of the p.Thr388Met variant is uncertain at this time. 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. Tzetis M et al. CFTR gene mutations--including three novel nucleotide substitutions--and haplotype background in patients with asthma, disseminated bronchiectasis and chronic obstructive pulmonary disease. Hum Genet. 2001 Mar;108(3):216-21. PMID: 11354633. -

Cystic fibrosis;C0238339:Hereditary pancreatitis;C0403814:Congenital bilateral aplasia of vas deferens from CFTR mutation;C2749757:Bronchiectasis with or without elevated sweat chloride 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.098
BayesDel_addAF	Uncertain	0.080	D
BayesDel_noAF	Pathogenic	0.19
Cadd	Uncertain	24
Dann	Uncertain	0.99
DEOGEN2	Uncertain	0.57	D;.;.;T;.
Eigen	Benign	0.16
Eigen_PC	Uncertain	0.27
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Uncertain	0.90	D;D;D;D;D
M_CAP	Pathogenic	0.42	D
MetaRNN	Benign	0.29	T;T;T;T;T
MetaSVM	Uncertain	0.24	D
MutationAssessor	Benign	1.3	L;.;.;.;L
MutationTaster	Benign	1.0	D;D
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-1.1	N;.;.;N;.
REVEL	Uncertain	0.60
Sift	Benign	0.11	T;.;.;T;.
Sift4G	Benign	0.12	T;.;.;T;.
Polyphen		0.65	P;.;.;.;.
Vest4		0.80
MVP		0.99
MPC		0.0054
ClinPred		0.053	T
GERP RS		4.7
Varity_R		0.18
gMVP		0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs143860237; hg19: chr7-117182116;