<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: collapse; ">Hi, </span><div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; ">I've been using the Variant Effect Predictor script but am confused by the Condel Score. The Ensembl Variation webpage documents the Condel score as this:</div><div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; ">" <span class="Apple-style-span" style="color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; font-size: 13px; ">The Condel authors provided us with a version specialised for finding a consensus between SIFT and PolyPhen and we integrated this into the variation API."</span></div><div style="border-collapse: collapse; "><font class="Apple-style-span" color="#555555" face="'Luxi Sans', Helvetica, Arial, Geneva, sans-serif" size="3"><span class="Apple-style-span" style="font-size: 13px; "><br></span></font></div><div style="border-collapse: collapse; ">However, I have noticed several examples of variant annotations where the Condel score is deleterious when both SIFT & Polyphen are tolerated/benign. For example: </div><div style="border-collapse: collapse; "><span class="Apple-style-span" style="border-collapse: collapse; ">SIFT=tolerated(0.13);PolyPhen=benign(0);Condel=deleterious(0.871)</span><span class="Apple-style-span" style="border-collapse: collapse; "><br></span></div><div style="border-collapse: collapse; ">(variant <span class="Apple-style-span" style="font-family: Calibri; font-size: 14px; ">1_1263085_G/A)</span></div><div style="border-collapse: collapse; "><span class="Apple-style-span" style="font-family: Calibri; font-size: 14px; "><br></span></div><div style="border-collapse: collapse; "><font class="Apple-style-span" face="Calibri" size="4"><span class="Apple-style-span" style="font-size: 14px; ">This leads me to believe that Condel is taking other factors into consideration besides just the Polyphen and SIFT score..do you have any information about this?</span></font></div><div style="border-collapse: collapse; "><font class="Apple-style-span" face="Calibri" size="4"><span class="Apple-style-span" style="font-size: 14px; "><br></span></font></div><div style="border-collapse: collapse; "><font class="Apple-style-span" face="Calibri" size="4"><span class="Apple-style-span" style="font-size: 14px; ">Thanks,</span></font></div><div style="border-collapse: collapse; "><font class="Apple-style-span" face="Calibri" size="4"><span class="Apple-style-span" style="font-size: 14px; "><br></span></font></div><div style="border-collapse: collapse; "><font class="Apple-style-span" face="Calibri" size="4"><span class="Apple-style-span" style="font-size: 14px; ">Paige Taylor</span></font></div><div style="border-collapse: collapse; "><font class="Apple-style-span" face="Calibri" size="4"><span class="Apple-style-span" style="font-size: 14px; "><br></span></font></div><div style="border-collapse: collapse; "><font class="Apple-style-span" face="Calibri" size="4"><span class="Apple-style-span" style="font-size: 14px; "><div style="font-family: Helvetica; font-size: medium; ">Paige Taylor<br><a href="mailto:sptaylor@ucla.edu">sptaylor@ucla.edu</a><br>Graduate Student Researcher<br>Stanley Nelson Lab<br>University of California, Los Angeles</div><div><br></div></span></font></div><div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; "><table border="0" cellpadding="0" cellspacing="0" width="510" style="border-collapse: collapse; width: 510pt; position: static; z-index: auto; "><col width="510" style="width: 510pt; "><tbody></tbody></table></div><div><br></div><br><br>
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