rs78769542

chr7-117611650-G-Achr7-117611650-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 8P and 5B. PM1 PM5 PP5_Strong BP4 BS2

The NM_000492.4(CFTR):c.3209G>A(p.Arg1070Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000307 in 1,613,422 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1070W) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.00030 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00031 (6 hom.)
• Consequence: CFTR NM_000492.4 missense
• Clinical Significance: drug response reviewed by expert panel P:18 U:4 O:1
• Conservation: PhyloP100: 9.94

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 Uncertain_significance. Variant got 3 ACMG points.

• PM1: In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 8 uncertain in NM_000492.4
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr7-117611649-C-T is described in ClinVar as [drug_response]. Clinvar id is 53685.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=13, Likely_pathogenic=2, drug_response=1, Uncertain_significance=1}.
• PP5: Variant 7-117611650-G-A is Pathogenic according to our data. Variant chr7-117611650-G-A is described in ClinVar as [drug_response]. Clinvar id is 35866.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=4, Likely_pathogenic=4, drug_response=1, Pathogenic=13}. Variant chr7-117611650-G-A is described in Lovd as [Pathogenic]. Variant chr7-117611650-G-A is described in Lovd as [Pathogenic]. Variant chr7-117611650-G-A is described in Lovd as [Pathogenic]. Variant chr7-117611650-G-A is described in Lovd as [Likely_pathogenic]. Variant chr7-117611650-G-A is described in Lovd as [Likely_pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.019629806).. Strength limited to SUPPORTING due to the PP5.
• 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.3209G>A	p.Arg1070Gln	missense_variant	20/27	ENST00000003084.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFTR	ENST00000003084.11	c.3209G>A	p.Arg1070Gln	missense_variant	20/27	1	NM_000492.4	P2
	ENST00000456270.1	n.177+4579C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.000296 AC: 45 AN: 151944 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00767

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000610 AC: 153 AN: 250926 Hom.: 3 AF XY: 0.000782 AC XY: 106 AN XY: 135614

Gnomad AFR exome AF: 0.000246

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00467

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000441

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000309 AC: 451 AN: 1461360 Hom.: 6 Cov.: 31 AF XY: 0.000432 AC XY: 314 AN XY: 726980

Gnomad4 AFR exome AF: 0.000269

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000176

Gnomad4 SAS exome AF: 0.00451

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000225

Gnomad4 OTH exome AF: 0.000298

GnomAD4 genome AF: 0.000296 AC: 45 AN: 152062 Hom.: 0 Cov.: 31 AF XY: 0.000471 AC XY: 35 AN XY: 74332

Gnomad4 AFR AF: 0.000145

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00767

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000106 Hom.: 0

Bravo AF: 0.0000945

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000799 AC: 97

Asia WGS AF: 0.00231 AC: 8 AN: 3478

EpiCase AF: 0.0000546

EpiControl AF: 0.00

ClinVar

Significance: drug response

Submissions summary: Pathogenic:18 Uncertain:4 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Cystic fibrosis Pathogenic:7 Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	Nov 05, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	The missense c.3209G>Ap.Arg1070Gln variant in CFTR gene has been reported previously in heterozygous state in individuals affected with Cystic Fibrosis Krasnov KV, et. al., 2008. Functional studies have shown that this variant decreases the open probability of the channel indiciating a mild functional impairment caused by the variant Seibert FS, et. al., 1996; Sosnay PR, et. al., 2013. The p.Arg1070Gln variant has been reported with allele frequency of 0.06% in gnomAD Exomes. This variant has been reported to the ClinVar database as Uncertain Significance / Likely Pathogenic / Pathogenic multiple submissions. The amino acid change p.Arg1070Gln in CFTR is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 1070 is changed to a Gln changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 25, 2024	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 1070 of the CFTR protein (p.Arg1070Gln). This variant is present in population databases (rs78769542, gnomAD 0.5%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with cystic fibrosis or congenital bilateral absence of the vas deferens. While this variant is commonly found in cis with p.Ser466*, it has also been observed without p.Ser466* in affected individuals and is expected to be causative for CFTR-related conditions whether p.Ser466* is present or not (PMID: 12955726, 18467194, 18951463, Invitae). Some individuals with this variant may present with milder symptoms. ClinVar contains an entry for this variant (Variation ID: 35866). 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 with a negative predictive value of 80%. Experimental studies have shown that this missense change affects CFTR function (PMID: 8662892, 8702904, 11242048, 23891399). This variant disrupts the p.Arg1070 amino acid residue in CFTR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7539342, 16189704, 21520337, 23974870). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Oct 05, 2021	The p.R1070Q pathogenic mutation (also known as c.3209G>A), located in coding exon 20 of the CFTR gene, results from a G to A substitution at nucleotide position 3209. The arginine at codon 1070 is replaced by glutamine, an amino acid with highly similar properties. Functional studies have shown that this mutation does not affect protein processing (Seibert FS et al. J. Biol. Chem., 1996 Jun;271:15139-45; Sosnay PR et al. Nat. Genet., 2013 Oct;45:1160-7), but it was observed to decrease the open probability of the channel (Seibert FS et al. J. Biol. Chem., 1996 Jun;271:15139-45). This mutation has been reported as a variant of varying clinical consequence (VVCC) (Sosnay PR et al. Pediatr. Clin. North Am., 2016 08;63:585-98; The Clinical and Functional TRanslation of CFTR (CFTR2); available at http://cftr2.org. Accessed March 30, 2018); when in trans with a second disease causing mutation it may result in cystic fibrosis, CFTR-related disorders, or no phenotype (Bombieri C et al. Semin Respir Crit Care Med, 2015 Apr;36:180-93; Girardet A et al. Eur. J. Hum. Genet., 2016 Apr;24:469-78). Of note, this mutation has also been observed as part of a complex allele with p.S466* (Krasnov KV et al. Hum. Mutat., 2008 Nov;29:1364-72; Lucarelli M et al. Mol. Med., 2015 Apr;21:257-75). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, The Hospital for Sick Children	Aug 29, 2019	- -
Likely pathogenic, criteria provided, single submitter	literature only	Counsyl	May 18, 2014	- -
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, PM3, PM5, PP3, PP4, BS2 -
Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 18, 2023	Variant summary: CFTR c.3209G>A (p.Arg1070Gln) results in a conservative amino acid change located in the ABC transporter type 1, transmembrane domain (IPR011527) of 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 0.00061 in 251348 control chromosomes in the gnomAD database, including 3 homozygotes. This frequency is not significantly higher than expected for a pathogenic variant in CFTR causing Non-classic Cystic Fibrosis (0.00061 vs 0.013), allowing no conclusion about variant significance. This variant has been reported in several patients with classic CF, non-classic CF, or CBAVD and in several patients it was observed in cis with p.S466X forming a complex allele (example, Krasnov_2008, Mercier_1994, Kanavakis_1005, Savov_1994, Tzetis_2007, Feldmann_2003, Sosnay_2013, Furlan_2016, Lucarelli_2015, Palermo_2016, Behar_2017, Ivanov_2018, Salvatore_2019, Frentescu_2008, Noni_2023). Available patient data suggests that in compound heterozygotes, this variant typically results in mild disease such as CF/NC and/or CBAVD, while in cis with p.S466X variant, it causes classic CF (Krasnov_2008). However, the variant has also been reported in trans with F508del in a CF patient with sweat chloride levels >60 mmol/L (without p.S466X in cis; Noni_2023). Although this variant is able to mature and reach the cell surface and was found to have no significant effect on chloride transport, it was found to cause relatively subtle channel defects with functional consequences of a lower open probability of the channel, lower cyclic AMP-stimulated iodide efflux, and lower bicarbonate transport (Seibert_1996, Krasnov_2008, Sosnay_2013, Choi_2001). In these studies, maturation assays were performed on HEK-293, MDCK and COS cells, and channel function and channel transport assays were performed on HEK293 and CHO cells. In FRT cells, however, chloride transport as well as maturation was found to be significantly reduced for this variant (20.5% of normal but increased to 32.9% of normal after Ivacaftor treatment) (Van Goor_2014). These functional differences might be due to the use of different cell lines in different studies and technical backgrounds; however, all of these studies are suggestive of a mild functional impairment for the variant in isolation. Multiple clinical laboratories have classified this variant with conflicting assertions: (n=8), likely pathogenic (n=2), and VUS (n=4), while the CFTR2 database has classified this variant as having varying clinical consequences. The variant's presence in cis with a truncating mutation, its association with CF/NC, CBAVD or other CFTR-RDs, and frequency data in South Asian are suggestive of a variable penetrance associated with this variant. A recent publication of policy recommendations towards improvement of the best practice guidelines for preimplantation genetic diagnosis of CF also reports this variant as a 'common variant with varying or indeterminate clinical consequences' (Girardet_2015). Due to the varying and typically mild disease phenotypes in individuals with this variant, as well as the allele frequency and presence of homozygotes in the gnomAD database, this variant likely represents a hypomorphic allele and was classified as likely pathogenic. -

not provided Pathogenic:5 Uncertain:1

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 22, 2018	The c.3209G>A; p.Arg1070Gln variant (rs78769542) has been observed in the compound heterozygous state in patients diagnosed with cystic fibrosis with pancreatic insufficiency (see link to CFTR2 database), or mild and atypical CFTR-related disorders, such as chronic pancreatitis and congenital absence of vas deferens (Feldmann 2003, Krasnov 2008), but its effects in the homozygous state are unknown. It is reported as pathogenic or likely pathogenic by several laboratories in Clinvar (Variation ID: 35866) and is observed in the South Asian population at an overall frequency of 0.46% (141/ 30766 alleles, 3 homozygotes) in the Genome Aggregation Database. The arginine at codon 1070 is highly conserved and computational algorithms (PolyPhen-2, SIFT) predict that the variant has an impact on the protein. Functional characterization of the variant protein is inconclusive on the expression level of the mature protein (Cotten 1996, Seibert 1996, Sosnay 2013, Van Goor 2014), but indicates an observable decrease in anion transport activity (Choi 2001, Seibert 1996, Sosnay 2013, Van Goor 2014). Based on available information, the p.Arg1070Gln variant is classified as pathogenic, with a variable presentation of clinical phenotypes. References: Link to CFTR2 database: https://www.cftr2.org/ Choi J et al. Aberrant CFTR-dependent HCO3- transport in mutations associated with cystic fibrosis. Nature. 2001;410(6824):94-7. Cotten J et al. Effect of cystic fibrosis-associated mutations in the fourth intracellular loop of cystic fibrosis transmembrane conductance regulator. J Biol Chem. 1996;271(35):21279-84. Feldmann D et al. CFTR genotypes in patients with normal or borderline sweat chloride levels. Hum Mutat. 2003;22(4):340. Krasnov K et al. Localization studies of rare missense mutations in cystic fibrosis transmembrane conductance regulator (CFTR) facilitate interpretation of genotype-phenotype relationships. Hum Mutat. 2008;29(11):1364-72. Seibert F et al. Disease-associated mutations in the fourth cytoplasmic loop of cystic fibrosis transmembrane conductance regulator compromise biosynthetic processing and chloride channel activity. J Biol Chem. 1996;271(25):15139-45. 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. Van Goor F et al. Effect of ivacaftor on CFTR forms with missense mutations associated with defects in protein processing or function. J Cyst Fibros. 2014;13(1):29-36. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jun 21, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Apr 28, 2015	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Blueprint Genetics	Jul 24, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jul 07, 2023	The CFTR c.3209G>A (p.Arg1070Gln) variant has been reported in the published literature in individuals with cystic fibrosis (PMID: 7683628 (1993), 22658665 (2012), 30561903 (2019), 18951463 (2008), 29504914 (2018), 36272381 (2023)) and congenital bilateral absence of the vas deferens (CBAVD) (PMID: 12955726 (2003)). It was also found to cause a mild phenotype in the compound heterozygous state with a second CF-causing variant and was often associated with pancreatic insufficient CF in the presence of S466* variant in cis (PMID: 18951463 (2008), 22658665 (2012)). Published functional studies indicate that this variant affects chloride channel gating causing lower open probability of the channel and lower bicarbonate transport (PMID: 8662892 (1996), 11242048 (2001)). The frequency of this variant in the general population, 0.0047 (143/30596 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2022	CFTR: PS3, PS4, PP4:Moderate, PP3 -

CFTR-related disorder Pathogenic:2

Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, The Hospital for Sick Children	Aug 29, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Dec 05, 2023	The CFTR c.3209G>A variant is predicted to result in the amino acid substitution p.Arg1070Gln. This variant has been reported to be causative for cystic fibrosis (Mercier et al. 1993. PubMed ID: 7683628; Krasnov et al. 2008. PubMed ID: 18951463; Mickle et al. 2000. PubMed: 10762539; www.CFTR2.org). This variant is reported in 0.47% of alleles in individuals of South Asian descent in gnomAD. This variant is interpreted as pathogenic. -

Obstructive azoospermia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Institute of Reproductive Genetics, University of Münster

Mar 16, 2022

- -

Cystic fibrosis;na:CFTR-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

curation

CFTR-France

Jul 03, 2015

when the variant is in trans with another CF-causing variation, can either result in CF or in a CFTR-RD -

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

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

-

- -

Bronchiectasis with or without elevated sweat chloride 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Oct 31, 2023

- -

ivacaftor response - Efficacy Other:1

drug response, reviewed by expert panel

curation

PharmGKB

Mar 24, 2021

PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance. Drug-variant association: Efficacy

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.40
BayesDel_addAF	Uncertain	0.084	D
BayesDel_noAF	Pathogenic	0.35
Cadd	Pathogenic	32
Dann	Pathogenic	1.0
DEOGEN2	Uncertain	0.48	T;.;.;T;.
Eigen	Pathogenic	0.73
Eigen_PC	Pathogenic	0.77
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Pathogenic	0.99	D;D;D;D;D
M_CAP	Pathogenic	0.50	D
MetaRNN	Benign	0.020	T;T;T;T;T
MetaSVM	Uncertain	0.45	D
MutationAssessor	Benign	0.99	L;.;.;.;.
MutationTaster	Benign	1.0	A;A
PrimateAI	Uncertain	0.77	T
PROVEAN	Benign	-0.14	N;.;.;N;.
REVEL	Pathogenic	0.70
Sift	Benign	0.42	T;.;.;T;.
Sift4G	Pathogenic	0.0	D;.;.;D;.
Polyphen		1.0	D;.;.;.;.
Vest4		0.87
MVP		0.99
MPC		0.0084
ClinPred		0.068	T
GERP RS		5.7
Varity_R		0.62
gMVP		0.95

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs78769542; hg19: chr7-117251704;