ClinVar Miner

Submissions for variant NM_000492.4(CFTR):c.53+1G>T

dbSNP: rs397508746
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CFTR2 RCV000047179 SCV000245957 pathogenic Cystic fibrosis 2017-03-17 reviewed by expert panel research
Counsyl RCV000047179 SCV000220810 likely pathogenic Cystic fibrosis 2014-10-16 criteria provided, single submitter literature only
Mendelics RCV000047179 SCV000886241 pathogenic Cystic fibrosis 2018-11-05 criteria provided, single submitter clinical testing
CFTR-France RCV000047179 SCV001169320 pathogenic Cystic fibrosis 2018-01-29 criteria provided, single submitter curation
Invitae RCV000047179 SCV003440157 pathogenic Cystic fibrosis 2024-01-29 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 1 of the CFTR gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CFTR are known to be pathogenic (PMID: 1695717, 7691345, 9725922). This variant is present in population databases (rs397508746, gnomAD 0.003%). Disruption of this splice site has been observed in individual(s) with cystic fibrosis and/or pancreatic insufficiency (PMID: 16596947, 22658665, 31126253, 32429104). This variant is also known as 185+1G>T. ClinVar contains an entry for this variant (Variation ID: 53988). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine RCV000047179 SCV004047463 pathogenic Cystic fibrosis criteria provided, single submitter clinical testing The splice site variant c.53+1G>T in CFTR gene has been observed in affected individuals (Krenkova P et.al.,2013). This variant has been reported to the ClinVar database as Pathogenic. The c.53+1G>T variant is novel (not in any individuals) in 1000 Genomes and allele frequency of 0.0004% is reported in gnomAD. The variant affects an invariant splice nucleotide and is expected to cause loss of function. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic.
Natera, Inc. RCV001826691 SCV002080061 pathogenic CFTR-related disorders 2017-03-17 no assertion criteria provided clinical testing

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