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Table 3 Likelihood ratio in favor of causality for selected neutral variants

From: A simple method for co-segregation analysis to evaluate the pathogenicity of unclassified variants; BRCA1 and BRCA2 as an example

Gene

HGVS1

traditional2

protein

# fam3

LR per family4

LR-variant5

BRCA1

c.135-15_135-12del6

IVS4-15delCTTT

p.=

19

3.8592 (2+)

3.8592

BRCA1

c.2613G>A7

2732G>A

p.Pro871Pro

1

1.8533(2+)

1.8533

BRCA1

c.5152+20T>A7

IVS18+20T>A

p.=

1

3.6711(1+; 1+)

3.6711

BRCA2

c.125A>G8

353A>G

p.Y42C

2

0.9728(2+)

0.7405

     

0.7612(1+; 4+)

 
  1. 1–5 For clarification see Table 1.
  2. These variants are regarded to be neutral towards cancer risk based on 6Vreeswijk et al. [15], 7Splice site prediction analysis and 8Goldgar et al. [3].
  3. 9 Pedigree is shown in Additional file 1; Figure S4.