ClinVar Miner

Submissions for variant NM_000492.4(CFTR):c.2490+1G>T

dbSNP: rs141158996
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Johns Hopkins Genomics, Johns Hopkins University RCV001250517 SCV001425311 pathogenic Cystic fibrosis 2020-03-09 criteria provided, single submitter clinical testing CFTR c.2490+1G>T has been previously identified in a patient with cystic fibrosis. This CFTR variant (rs141158996) is rare (<0.1%) in a large population dataset (gnomAD: 1/190386 total alleles; 0.0005%; no homozygotes). This variant destroys a canonical splice donor site and is predicted to cause abnormal gene splicing. We consider this variant to be pathogenic.
Invitae RCV001250517 SCV003480730 pathogenic Cystic fibrosis 2022-06-10 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 973859). This variant is also known as c.2622+1G>T. Disruption of this splice site has been observed in individuals with cystic fibrosis (PMID: 7683952, 9239681, 12815607, 20059485, 23974870). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change affects a donor splice site in intron 14 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).
PreventionGenetics, part of Exact Sciences RCV003898246 SCV004712081 pathogenic CFTR-related condition 2023-12-21 criteria provided, single submitter clinical testing The CFTR c.2490+1G>T variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant was reported in individuals undergoing genetic testing for cystic fibrosis (referred to as c.2622+1G>T in Scotet et al. 2003. PubMed ID: 12815607; Table S4, Raraigh et al. 2021. PubMed ID: 34782259). This variant is reported in 0.0011% of alleles in individuals of European (non-Finnish) descent in gnomAD and is interpreted as pathogenic in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/973859/). Variants that disrupt the consensus splice donor site in CFTR are expected to be pathogenic. This variant is interpreted as pathogenic.

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