ClinVar Miner

Submissions for variant NM_000492.3(CFTR):c.2559T>C (p.Ile853=) (rs1800104)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000593086 SCV000883567 likely benign not provided 2017-05-19 criteria provided, single submitter clinical testing The CFTR c.2559T>C, p.Ile853Ile variant (rs1800104) has not been reported in the medical literature or gene-specific variant databases. It is observed in the general population databases at a frequency of 0.06 percent in the 1000 Genomes Project (3/5008 alleles), 0.02 percent in the Exome Variant Server (2/13006 alleles), and 0.03 percent in the Genome Aggregation Database (88/277070 alleles). The variant is a synonymous substitution, and computational algorithms (GeneSplicer, Human Splicing Finder, MaxEntScan, MutationTaster, NetGene2, NNSplice, SpliceSiteFinder-like) predict that the variant has no impact on splicing. Based on the above information, the variant is considered likely benign.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000593086 SCV000702203 uncertain significance not provided 2016-09-27 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000281657 SCV000466518 uncertain significance Cystic fibrosis 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000781229 SCV000919133 uncertain significance not specified 2018-01-26 criteria provided, single submitter clinical testing Variant summary: The CFTR c.2559T>C (p.Ile853Ile) variant involves the alteration of a non-conserved nucleotide causing a synonymous change and 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts alterations to ESE binding. However, these predictions have yet to be confirmed by functional studies. This variant was found in 88/277110 control chromosomes (gnomAD and publication controls) at a frequency of 0.0003176, which does not exceed the estimated maximal expected allele frequency of a pathogenic CFTR variant (0.0129603). Multiple publications have cited the variant with limited information. In addition, multiple clinical diagnostic laboratories/reputable databases have cited the variant with conflicting classifications, "likely benign" or "uncertain significance." Taken together, this variant is classified as a "Variant of Uncertain Significance - Possibly Benign."
Invitae RCV000281657 SCV000625733 likely benign Cystic fibrosis 2017-05-15 criteria provided, single submitter clinical testing

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