<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Oh, whoops! Indeed that's correct! If you visualize them on UCSC (click the UCSC link on the 3 pages: e.g. <a href="http://exac.broadinstitute.org/variant/1-245133629-A-C">http://exac.broadinstitute.org/variant/1-245133629-A-C</a>), you'll notice that they fall into splice variants that affect 3' and 5' UTRs, which are unlikely to be LoF (will not trigger nonsense-mediated decay).</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">This is a newer version of LOFTEE that hasn't been made into a full release yet, so hasn't been integrated into the ExAC browser yet.</div> <br> <div id="bloop_sign_1458601101007142912" class="bloop_sign"><div style="font-family:helvetica,arial;font-size:13px">-Konrad</div></div> <br><p class="airmail_on">On March 21, 2016 at 6:44:18 PM, Wei Zhao (<a href="mailto:mikezhaow@gmail.com">mikezhaow@gmail.com</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div><div></div><div>
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<div>Thank you, Konrad!<br>
<br></div>
I listed the annotation for the three variant-transcript pairs
below:<br>
<br>
var273214
1:245133629
G ENSG00000203666
ENST00000366523 Transcript
splice_acceptor_variant -
-
-
-
-
-
LoF=LC;LoF_flags=;IMPACT=HIGH;LoF_filter=5UTR_SPLICE;LoF_info=INTRON_SIZE:285;STRAND=1<br>
var78183
8:130789839
C ENSG00000147697
ENST00000276708 Transcript
splice_acceptor_variant -
-
-
-
-
-
LoF_filter=3UTR_SPLICE;IMPACT=HIGH;LoF_flags=;LoF=LC;LoF_info=INTRON_SIZE:8419;STRAND=-1<br>
var113394
5:177474136
C ENSG00000204677
ENST00000511189 Transcript
splice_donor_variant
-
-
-
-
-
-
LoF_info=INTRON_SIZE:1531;LoF_filter=3UTR_SPLICE;LoF_flags=;LoF=LC;IMPACT=HIGH;STRAND=1<br>
<br></div>
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