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Table 1 Summary of rules for calculating sequence deleteriousness score δ(g)

From: SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing

SV class t  SV tSV SVe
Coding or splice UTR Intronic Promoter
DEL 1 1 {0.8, 1} 0 ≤ δ(g)≤1 0 0.4
DUP 1a 0 {0.8, 1} 0 ≤ δ(g)≤1 0 0.4
INV 0 1 1 0 ≤ δ(g)≤1 0 0.4
INS {0.2, 0.9} 0 ≤ δ(g)≤1 0 0.4
BND 1 1 1 0.4
  1. Higher scores indicate a greater degree of predicted deleterious effect on transcript function. tSV: The SV fully contains the transcript in question. tSV: Partial overlap of the transcript and the SV. SVe The SV is completely contained within the indicated sequence element. {0.8, 1} and {0.2, 0.9} indicate scores for {in-frame, frameshift} variants
  2. aDuplication of the entire gene is assigned a score of 1, triplication is assigned a score of 2, and so on