ClinVar Miner

Submissions for variant NM_000492.3(CFTR):c.4242+13A>G (rs76179227)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000079005 SCV000603039 benign not specified 2017-01-18 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000079005 SCV000110874 benign not specified 2013-04-29 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587429 SCV000697015 benign not provided 2016-06-28 criteria provided, single submitter clinical testing Variant summary: The CFTR c.4242+13A>G variant involves the alteration of a non-conserved intronic nucleotide at a position not widely known to affect normal splicing. One in silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict the variant not to affect splicing, and this prediction is supported by a minigene splicing assay showing no abnormal RNA products from a minigene containing this intronic variant. This variant was found in 424/120694 control chromosomes (including 1 homozygote), predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.0051196 (333/65044). This frequency is less than the estimated maximal expected allele frequency of a pathogenic CFTR variant (0.0129603), and it cannot be ruled out that the homozygote could be affected since the ExAC cohort is a general population cohort rather than a healthy or disease-free cohort. Although this variant is found at a frequency less than the most common pathogenic CFTR variant, DeltaF508 (allele frequency in ExAC of 823/121296), c.4242+13A>G is found at a frequency greater than 2-fold higher than the second most common pathogenic CFTR variant in ExAC, c.350G>A (p.Arg117His; 185/120360), highly suggesting that c.4242+13A>G is not pathogenic.Although the variant has been found in patients reported in the literature, there are no reports that show the variants clear-cut causal role in CF and/or CBAVD. In other CFTR-RD phenotypes (asthma, DB, and COPD), this variant was observed at similar frequencies in cases and controls, supporting the notion that it is not a risk factor for these milder phenotypes either. To our knowledge, there was only one report of the variant co-occurring with a pathogenic variant, c.5T_TG11, in a diffuse bronchiectasis patient; however, c.-1043dupT (not in ClinVar and not yet internally classified) was also identified in this patient, phase of these variants was not specified, segregation studies were not performed, and authors consider the variant of interest to be a polymorphism since functional studies showed no effect on splicing (Bergougnoux_JCF_2015). Additionally, UMD reports the variant as a complex allele with c.2538G>A (p.Trp846X) and c.1521_1523delCTT (p.Phe508del) on the other allele in an individual with CF (unpublished reference), suggesting that the variant of interest is not causative in this patient. Furthermore, multiple papers as well as Emory Genetics lab via ClinVar and SickKids report the variant as a benign polymorphism. Taken together, this intronic CFTR variant has been classified as Benign.
Invitae RCV000233025 SCV000285006 benign Cystic fibrosis 2017-12-28 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000079005 SCV000270059 benign not specified 2017-07-31 criteria provided, single submitter clinical testing c.4242+13A>G in intron 26 of CFTR: This variant is not expected to have clinical significance because it has been identified in 1.6% (159/10116) of Ashkenazi Je wish chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broa dinstitute.org; dbSNP rs76179227). It was also identified in 5 homozygotes in gn omAD.
PreventionGenetics RCV000079005 SCV000304496 likely benign not specified criteria provided, single submitter clinical testing

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