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

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

	No filters	Complete filters^a	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 NS^b sequence changes (% [n])	20.63% (138)	21.74% (3)	+5%
Percentage of predicted ESEs affected by IFD^b sequence changes (% [n])	8.52% (57)	13.04% (3)	+53%
Percentage of predicted ESEs affected by M^b sequence changes (% [n])	1.64% (11)	8.70% (2)	+430%
Percentage of predicted ESEs affected by UV^b sequence changes predicted to be deleterious^c (% [n])	8.52% (57)	26.10% (6)	+206%
Percent of predicted ESEs affected by UV^b sequence changes predicted to be neutral^c (% [n])	18.83% (126)	8.70% (2)	-54%
Percent of predicted ESEs affected by P^b,d sequence changes (% [n])	4.19% (28)	0.00% (0)	-100%

^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.

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