ClinVar Miner

Submissions for variant NM_000492.4(CFTR):c.853A>T (p.Ile285Phe)

gnomAD frequency: 0.00145  dbSNP: rs151073129
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Total submissions: 11
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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 RCV000598331 SCV000697048 benign not specified 2021-01-22 criteria provided, single submitter clinical testing Variant summary: CFTR c.853A>T (p.Ile285Phe) results in a non-conservative amino acid change located in the ABC transporter type 1, transmembrane domain (IPR011527) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. In contrast, a recently published in-silico tools based consensus classifier has predicted this variant to have a neutral impact (Michels_2019). The variant allele was found at a frequency of 0.00043 in 280644 control chromosomes, predominantly at a frequency of 0.0046 within the African subpopulation in the gnomAD database, including 1 homozygote. The combined allele frequency of the two most frequent pathogenic CF variants in Africans (i.e. c.2988+1G>A and p.F508del) that are found in up to 60% of all carriers (see in PMID 21474639) is 0.0038 in the gnomAD database. Therefore, the allele frequency of c.853A>T alone is much higher than combined frequency of the two most common pathogenic variants in the same subpopulation, supporting a benign role for this variant. The variant, c.853A>T, has been reported in the literature in an individual with chronic respiratory problems and a non-informative genotype (example, Schrijver 2005) and in an individual reportedly affected with Cystic Fibrosis also with a non-informative genotype (example, Pereira 2019). It was also reported in trans with a large CFTR promoter deletion in a presumably unaffected mother of a CF proband. The molecular diagnosis of CF in the proband was attributed to two other variants, namely the promoter deletion inherited from the mother and c.2988+1G>A inherited from the father (Hantash_2006). These reports 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. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and classified the variant as likely benign (n=2)/benign (n=1). Based on the evidence outlined above, the variant was classified as benign.
Eurofins Ntd Llc (ga) RCV000598331 SCV000700536 likely benign not specified 2017-06-23 criteria provided, single submitter clinical testing
Mendelics RCV000029547 SCV001137469 benign Cystic fibrosis 2019-05-28 criteria provided, single submitter clinical testing
Invitae RCV000029547 SCV001597830 likely benign Cystic fibrosis 2024-01-29 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV002257363 SCV002529738 likely benign Hereditary pancreatitis 2020-11-09 criteria provided, single submitter curation
Ambry Genetics RCV000029547 SCV002675488 likely benign Cystic fibrosis 2022-10-21 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV002477015 SCV002774136 likely benign not provided 2021-08-25 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002477014 SCV002797967 likely benign Bronchiectasis with or without elevated sweat chloride 1; Cystic fibrosis; Hereditary pancreatitis; Congenital bilateral aplasia of vas deferens from CFTR mutation 2021-09-09 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV002477015 SCV003800282 likely benign not provided 2023-10-16 criteria provided, single submitter clinical testing
Johns Hopkins Genomics, Johns Hopkins University RCV000029547 SCV004024501 likely benign Cystic fibrosis 2023-07-14 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004532410 SCV004726993 likely benign CFTR-related disorder 2023-01-27 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).

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