Submissions for variant NM_000492.4(CFTR):c.489+3A>G

gnomAD frequency: 0.00016  dbSNP: rs377729736

Total submissions: 21

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000047162	SCV000075175	pathogenic	Cystic fibrosis	2024-01-31	criteria provided, single submitter	clinical testing	This sequence change falls in intron 4 of the CFTR gene. It does not directly change the encoded amino acid sequence of the CFTR protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs377729736, gnomAD 0.04%). This variant has been observed in individual(s) with cystic fibrosis, sarcoidosis, azoospermia, or congenital absence of the vas deference (PMID: 10980579, 11810271, 19893581, 20021716, 22020151). This variant is also known as 621+3A>G. ClinVar contains an entry for this variant (Variation ID: 53971). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of 4, but is expected to preserve the integrity of the reading-frame (PMID: 11810271). For these reasons, this variant has been classified as Pathogenic.
Eurofins Ntd Llc (ga)	RCV000507054	SCV000344240	uncertain significance	not provided	2017-11-22	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000507054	SCV000601124	likely pathogenic	not provided	2023-07-05	criteria provided, single submitter	clinical testing	The CFTR c.489+3A>G variant has been reported in the published literature in individuals with cystic fibrosis (CF) who carried a CFTR pathogenic variant on the opposite chromosome (PMID: 11810271 (2001)). It has also been observed in individuals with sarcoidosis (PMID: 10980579 (2000)), azoospermia (PMID: 20021716 (2009)), bronchiectasis (PMID: 33260873 (2020)), and congenital bilateral absence of the vas deferens (CBAVD) (PMID: 22020151 (2012)). However, it has also been observed in an asymptomatic individual who carried a CFTR pathogenic variant on the opposite chromosome (PMID: 1989381 (2010)). RNA studies have shown that it causes the synthesis of aberrantly spliced CFTR mRNA transcripts, but it does not prevent the synthesis of normally spliced CFTR mRNA (PMID: 11810271 (2001), 19893581 (2010)). The frequency of this variant in the general population, 0.0021 (23/11152 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper CFTR mRNA splicing. Based on the available information, this variant is classified as likely pathogenic.
GeneDx	RCV000507054	SCV000617530	uncertain significance	not provided	2017-07-28	criteria provided, single submitter	clinical testing	The c.489+3A>G variant in the CFTR gene, also referred to as c.621+3A>G, has been reported in the heterozygous state patients with sarcoidosis, CAVD, and azoospermia without CAVD (Bombieri et al., 2000; Amato et al., 2012; Gallati et al., 2009). This variant reduces the quality of the splice donor site in intron 4, and may cause abnormal gene splicing. The c.489+3A>G variant is observed in 30/50716 (0.06%) alleles in the ExAC dataset (Lek et al., 2016). We interpret c.489+3A>G as a variant of uncertain significance.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000047162	SCV000697029	likely pathogenic	Cystic fibrosis	2023-06-26	criteria provided, single submitter	clinical testing	Variant summary: CFTR c.489+3A>G (legacy name c.621+3A>G) alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 tools via Alamut predict that the variant abolishes or weakens the canonical 5' splicing donor site. This is further supported by experimental evidence reporting an impact on mRNA splicing as corroborated by two independent studies that showed a reproducible distribution of transcripts resulting from activation of an alternate splice site (approx 28.3%) and transcripts resulting from complete skipping of exon 4 (approx 6.8%) in addition to levels of wild-type transcripts (approx remaining 65%) (Tzetis_2001, Forzan_2010). Furthermore, the pattern of abnormal splicing demonstrated by this variant is very similar to that of c.489+1G>T (legacy name c.621+1G>T) considered to be a well-recognized pathogenic CFTR variant (Tzetis_2001) (ACMG PP3, PS3). The variant allele was found at a frequency of 0.00025 in 247812 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in CFTR causing Non-Classic Cystic Fibrosis (0.00025 vs 0.013), allowing no conclusion about variant significance. c.489+3A>G has been reported in the literature in individuals affected with Cystic Fibrosis (e.g. Tzetis_2001, Kanavakis_2003, Soltysova_2018, Claustres_2017) and other CFTR-related diseases such as CBAVD (e.g. Amato_2012), azoospermia (e.g. Gallati_2009), sarcoidosis (Bombieri_2000), and chronic pancreatitis (Sofia_2016). These data, when ascertained conservatively, limited to patients with a confirmed diagnosis of CF, support the notion that the variant is likely to be associated with disease (ACMG PP1, PM3). At least one report of an asymptomatic 8 year old girl harboring this variant in trans with another pathogenic CFTR variant (p.Q552*) has been ascertained (Forzan_2010). This patient had inconsistent sweat chloride levels ranging from 49-75 mEq/L in three independent measurements and the possibility of subclinical disease cannot be entirely ruled out. In addition, the variant was also reported to have been observed in cis with c.4332delTG (legacy name) in a CF patient harboring c.2183AA/G (legacy name) on the other allele (Loumi_2008) (ACMG BP2). However, to our knowledge, there are no additional reports of this co-occurrence to substantiate this finding. The CFTR2 database states this variant to have varying consequences. Multiple other ClinVar submitters cite the variant as pathogenic/likely pathogenic (n=7) or uncertain significance (n=7). Based on the evidence outlined above, the variant was classified as likely pathogenic for CF, mindful of the variable expressivity observed for this disorder.
Mendelics	RCV000047162	SCV000886393	uncertain significance	Cystic fibrosis	2018-11-05	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000047162	SCV000916177	uncertain significance	Cystic fibrosis	2018-12-07	criteria provided, single submitter	clinical testing	The CFTR c.489+3A>G variant, also referred to as c.621+3A>G, has been reported in six studies in which it is identified in a compound heterozygous state in at least six individuals and in a heterozygous state in at least five individuals with varying clinical consequences including cystic fibrosis, CBAVD, azoospermia, and sarcoidosis (Bombieri et al. 2000; Tzetis et al. 2001; Loumi et al. 2008; Gallati et al. 2009; Forzan et al. 2010; Amato et al. 2012). However, one study found that the frequency of affected individuals carrying the variant was lower than expected based on the allele frequency in the control population (Forzan et al. 2010). The c.489+3A>G variant occurs in the splice region and RT-PCR analysis revealed that the variant generates both correctly spliced and incorrectly spliced products, suggesting aberrant splicing with a possibility of some residual activity of the CFTR protein (Tzetis et al. 2001). The c.489+3A>G variant has been reported at a frequency of 0.000592 in the European (non-Finnish) population of the Exome Aggregation Consortium. Based on the conflicting evidence and the clinical variability found in patients with this variant, the c.489+3A>G variant is classified as a variant of unknown significance but suspicious for pathogenicity for CFTR-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV001001769	SCV001159395	uncertain significance	not specified	2019-04-06	criteria provided, single submitter	clinical testing	The CFTR c.489+3A>G variant (rs377729736), also known as 621+3A>G, is reported in the literature in individuals affected with cystic fibrosis, congenital bilateral absence of vas deferens (CBAVD), and sarcoidosis, including individuals with a severe pathogenic variant on the opposite chromosome (Amato 2012, Gallati 2009, Giuliani 2010, Sermet-Gaudelus 2010, Soltysova 2018, Tzetis 2001). However, this variant has also been reported in an asymptomatic individual who carries a pathogenic nonsense variant in trans (Forzan 2010), and in cis with a truncating variant in an individual with cystic fibrosis (Loumi 2008). This variant is reported in ClinVar (Variation ID: 53971), and is found in the general population with an overall allele frequency of 0.023% (63/276,630 alleles) in the Genome Aggregation Database. This is an intronic variant in a highly conserved nucleotide, and computational analyses (Alamut v.2.11) predict that this variant may impact splicing by weakening the nearby canonical donor splice site. Functional studies show aberrant mRNA splicing making up about 35% of transcripts, but it is unknown if this level altered transcripts is sufficient to cause disease (Forzan 2010, Tzetis 2001). Due to conflicting information, the clinical significance of the c.489+3A>G variant is uncertain at this time. References: Amato F et al. Extensive molecular analysis of patients bearing CFTR-related disorders. J Mol Diagn. 2012 Jan;14(1):81-9. Forzan M et al. Is CFTR 621+3 A>G a cystic fibrosis causing mutation? J Hum Genet. 2010 Jan;55(1):23-6. Gallati S et al. Cystic fibrosis transmembrane conductance regulator mutations in azoospermic and oligospermic men and their partners. Reprod Biomed Online. 2009 Nov;19(5):685-94. Giuliani R et al. Identification of the second CFTR mutation in patients with congenital bilateral absence of vas deferens undergoing ART protocols. Asian J Androl. 2010 Nov;12(6):819-26. Loumi O et al. CFTR mutations in the Algerian population. J Cyst Fibros. 2008 Jan;7(1):54-9. Epub 2007 Jun 14. Sermet-Gaudelus I et al. Measurement of nasal potential difference in young children with an equivocal sweat test following newborn screening for cystic fibrosis. Thorax. 2010 Jun;65(6):539-44. Soltysova A et al. Comprehensive genetic study of cystic fibrosis in Slovak patients in 25 years of genetic diagnostics. Clin Respir J. 2018 Mar;12(3):1197-1206. Tzetis M et al. Qualitative and quantitative analysis of mRNA associated with four putative splicing mutations (621+3A-->G, 2751+2T-->A, 296+1G-->C, 1717-9T-->C-D565G) and one nonsense mutation (E822X) in the CFTR gene. Hum Genet. 2001 Dec;109(6):592-601.
Baylor Genetics	RCV000047162	SCV001163477	likely pathogenic	Cystic fibrosis		criteria provided, single submitter	clinical testing
CFTR-France	RCV001009491	SCV001169586	pathogenic	CFTR-related disorders	2018-03-09	criteria provided, single submitter	curation
Ambry Genetics	RCV000047162	SCV001185048	uncertain significance	Cystic fibrosis	2022-12-02	criteria provided, single submitter	clinical testing	The c.489+3A>G intronic variant results from an A to G substitution 3 nucleotides after coding exon 4 in the CFTR gene. This variant (reported as 621+3G>A) was described in four Greek individuals with severe cystic fibrosis (CF), each with a second pathogenic mutation; however, the phase (cis/trans) of the these alterations is uncertain and deletion/duplication testing was not performed. Functional testing of the alteration showed a decrease in the number of normal CFTR transcripts (Tzetis M et al. Hum Genet. 2001;109(6):592-601). In contrast, other functional and clinical evidence suggest that this variant should not be considered a CF disease-causing mutation and further studies are needed to determine if this variant is associated with CBAVD or atypical CF (Forzan M et al. J Hum Genet. 2010;55(1):23-26). The c.489+3A>G alteration has been reported as a variant of varying clinical consequences (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 January 21, 2019). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Johns Hopkins Genomics, Johns Hopkins University	RCV000047162	SCV001371813	likely pathogenic	Cystic fibrosis	2020-01-29	criteria provided, single submitter	clinical testing	CFTR variant associated with variable clinical consequences. See www.CFTR2.org for phenotype information.
Genome-Nilou Lab	RCV000047162	SCV001822004	likely pathogenic	Cystic fibrosis	2021-07-22	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV002255273	SCV002529736	uncertain significance	Hereditary pancreatitis	2021-04-21	criteria provided, single submitter	curation
MGZ Medical Genetics Center	RCV000047162	SCV002580609	likely pathogenic	Cystic fibrosis	2022-01-13	criteria provided, single submitter	clinical testing
Eurofins-Biomnis	RCV002255273	SCV003935049	likely pathogenic	Hereditary pancreatitis	2022-10-20	criteria provided, single submitter	clinical testing
Institute of Human Genetics, University of Leipzig Medical Center	RCV000047162	SCV004100705	pathogenic	Cystic fibrosis	2023-09-25	criteria provided, single submitter	clinical testing	Criteria applied: PM3_VSTR,PS3_SUP,PP4
PreventionGenetics, part of Exact Sciences	RCV003407425	SCV004110708	likely pathogenic	CFTR-related condition	2022-11-18	criteria provided, single submitter	clinical testing	The CFTR c.489+3A>G variant is predicted to interfere with splicing. This variant has been reported in patients with cystic fibrosis, congenital bilateral absence of vas deferens (CBAVD), azoospermia, or sarcoidosis, including in patients with a pathogenic variant on the opposite chromosome (Amato et al. 2011. PubMed ID: 22020151; Bombieri et al. 2000. PubMed ID: 10980579; Gallati et al. 2009. PubMed ID: 20021716; Giuliani et al. 2010. PubMed ID: 20657600; Kanavakis et al. 2003. PubMed ID: 12752573; Sermet-Gaudelus et al. 2010. PubMed ID: 20522854; Soltysova et al. 2017. PubMed ID: 28544683; Tzetis et al. 2001. PubMed ID: 11810271). This variant was also reported in trans with a second pathogenic variant in an asymptomatic female child; however, her sweat chloride testing suggested possible subclinical disease (49-75 mEq/L) (Forzan et al. 2009. PubMed ID: 19893581). Additionally, functional studies demonstrate that this variant leads to aberrant splicing with a defect consistent with other known splicing variants at this location (c.489+1G>T aka 621+1G>T; Tzetis et al. 2001. PubMed ID: 11810271; Forzan et al. 2009. PubMed ID: 19893581). This variant is reported in 0.039% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/7-117171171-A-G). Taken together, this variant is interpreted as likely pathogenic.
Baylor Genetics	RCV003474605	SCV004213263	likely pathogenic	Bronchiectasis with or without elevated sweat chloride 1	2023-10-27	criteria provided, single submitter	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000507054	SCV001979366	uncertain significance	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000507054	SCV001980455	uncertain significance	not provided		no assertion criteria provided	clinical testing