A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer

Table 3 Variants predicted by SNPfold to affect UTR structure

Class^a	Patient ID	Gene	mRNA	UTR position	rsID (dbSNP 142)	Rank^e	p-value
Class^a	Patient ID	Gene	mRNA	UTR position	Allele Frequency (%)^d	Rank^e	p-value
F	In 26 patients	BRCA2 ^b	c.-52A > G	5’ UTR	rs206118	2/900	0.002
F	In 26 patients	BRCA2 ^b	c.-52A > G	5’ UTR	14.86	2/900	0.002
F	In 40 patients	BRCA2 ^b	c.*532A > G	3’ UTR	rs11571836	239/2700	0.089
F	In 40 patients	BRCA2 ^b	c.*532A > G	3’ UTR	19.75	239/2700	0.089
P	7-4C	CDH1 ^c	c.-71C > G	5’ UTR	rs34033771	69/600	0.115
P	7-4C	CDH1 ^c	c.-71C > G	5’ UTR	0.56	69/600	0.115
F	4-2E	TP53 ^b	c.*485G > A	3’ UTR	rs4968187	169/4500	0.038
	5-4A				rs4968187
	5-4A				5.11
F	2-1A, 7-1B, 5-2A.7-1D, 7-2B, 7-2F	TP53 ^b	c.*826G > A	3’ UTR	rs17884306	371/4500	0.082
	7-4C				rs17884306
	7-4C				5.71

^aF:Flagged; P:Prioritized
^bLong Range UTR SNPfold Analysis
^cLocal Range SNPfold Analysis
^dIf available
^eRank of the SNP, in terms of how much it changes the mRNA structure compared to all other possible mutations

ISSN: 1755-8794