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Table 4 Effect of filters on colocalization of predicted ESEs with reported sequence changes in the BRCA1 open reading frame

From: Evolutionary conservation analysis increases the colocalization of predicted exonic splicing enhancers in the BRCA1gene with missense sequence changes and in-frame deletions, but not polymorphisms

  No filters Complete filtersa Percentage change from no filters to complete filters
Number of predicted ESEs 669 23 -
Percentage of predicted ESEs affected by sequence changes (% [n]) 51.72% (346) 60.87% (14) +17%
Percentage of predicted ESEs affected by NSb sequence changes (% [n]) 20.63% (138) 21.74% (3) +5%
Percentage of predicted ESEs affected by IFDb sequence changes (% [n]) 8.52% (57) 13.04% (3) +53%
Percentage of predicted ESEs affected by Mb sequence changes (% [n]) 1.64% (11) 8.70% (2) +430%
Percentage of predicted ESEs affected by UVb sequence changes predicted to be deleteriousc (% [n]) 8.52% (57) 26.10% (6) +206%
Percent of predicted ESEs affected by UVb sequence changes predicted to be neutralc (% [n]) 18.83% (126) 8.70% (2) -54%
Percent of predicted ESEs affected by Pb,d sequence changes (% [n]) 4.19% (28) 0.00% (0) -100%
  1. aIncreased threshold, location within 125 nucleotides of exon end and conserved in human, primate, mouse, cow, dog and opossum. bClassification in Breast Cancer Information Core (BIC) database: IFD, in-frame deletion; M, missense; M-UV, missense unclassified sequence variant; NS, nonsense. cDeleterious refers to amino acid sequence changes predicted most likely to affect protein structure and function. dP, polymorphisms include those reported in BIC and SNPper. ESE, exonic splicing enhancer.