Boundary mismatch for ACMG scores

[leshaker]

Hello again,
while working with your code I just discovered that the boundaries for translating ACMG scores into classes seems to be inaccurate.

While the paper and your docs state

the tcl code uses

		    if {$g_rankingScore($AnnotSV_ID) eq ""} {
			set class "NA"
		    } elseif {$g_rankingScore($AnnotSV_ID) >= "0.99"} {
			set class 5
		    } elseif {$g_rankingScore($AnnotSV_ID) >= "0.9"} {
			set class 4
		    } elseif {$g_rankingScore($AnnotSV_ID) >= "-0.9"} {
			set class 3
		    } elseif {$g_rankingScore($AnnotSV_ID) >= "-0.99"} {
			set class 2
		    } else {
			set class 1
		    }

AnnotSV/share/tcl/AnnotSV/AnnotSV-write.tcl

Line 1459 in c5dff6a

} elseif {$g_rankingScore($AnnotSV_ID) >= "-0.9"} {

thus CNVs with score -0.90 are treated as VUS while they should be Likely Benign

Could you please double check if my observation is correct?

thanks!
Max

[lgmgeo]

You're absolutely rigth.
This has been fixed in the patch_AnnotSV branch:

		    if {$g_rankingScore($AnnotSV_ID) eq ""} {
			set class "NA"
		    } elseif {$g_rankingScore($AnnotSV_ID) >= "0.99"} {
			set class 5
		    } elseif {$g_rankingScore($AnnotSV_ID) >= "0.90"} {
			set class 4
		    } elseif {$g_rankingScore($AnnotSV_ID) >= "-0.89"} {
			set class 3
		    } elseif {$g_rankingScore($AnnotSV_ID) >= "-0.98"} {
			set class 2
		    } else {
			set class 1
		    }

Really sorry for the inconvenience.

[lgmgeo]

AnnotSV v3.5 is posted