ClinVar Miner

Submissions for variant NM_000492.4(CFTR):c.164+9A>T

dbSNP: rs397508245
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001264463 SCV001442632 uncertain significance not specified 2020-10-12 criteria provided, single submitter clinical testing Variant summary: CFTR c.164+9A>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. At-least one in-silico prediction tool, Transcript-inferred Pathogenicity score (TraP) predicts a benign outcome for this variant. The variant allele was found at a frequency of 1.2e-05 in 248920 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.164+9A>T has been reported in the literature in at-least one individual among Turkish Cystic Fibrosis chromosomes and has been subsequently cited by others (example, Onay_1998, Bobadilla_2002, Singh_2015, Bickmann_2009). These report(s) do not provide unequivocal conclusions about association of the variant with Cystic Fibrosis. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.
Invitae RCV000576924 SCV001707039 likely benign Cystic fibrosis 2024-01-05 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000576924 SCV001821982 uncertain significance Cystic fibrosis 2021-07-22 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001588870 SCV001821983 uncertain significance Congenital bilateral aplasia of vas deferens from CFTR mutation 2021-07-22 criteria provided, single submitter clinical testing
Ambry Genetics RCV000576924 SCV002703059 likely benign Cystic fibrosis 2022-06-16 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
PreventionGenetics, part of Exact Sciences RCV004537224 SCV004740095 likely benign CFTR-related disorder 2019-04-02 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
ClinVar Staff, National Center for Biotechnology Information (NCBI) RCV000576924 SCV000678915 not provided Cystic fibrosis no assertion provided literature only

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