<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><p style="box-sizing: border-box; margin-bottom: 16px; color: rgb(36, 41, 46); font-family: -apple-system, system-ui, "Segoe UI", Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; font-size: 14px; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255); margin-top: 0px !important;" class="">Hi,</p><p style="box-sizing: border-box; margin-top: 0px; margin-bottom: 16px; color: rgb(36, 41, 46); font-family: -apple-system, system-ui, "Segoe UI", Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; font-size: 14px; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class="">Thanks for this report, it is an issue we are aware of. As you probably know, not all RefSeq transcripts completely match the reference genome. In cases where they don't, we are now using alignment files provided by NCBI to create a new reference, matching the transcript, and use this for consequence calling.</p><p style="box-sizing: border-box; margin-top: 0px; margin-bottom: 16px; color: rgb(36, 41, 46); font-family: -apple-system, system-ui, "Segoe UI", Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; font-size: 14px; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class="">Our HGVS calculation does not currently use this reference modification, but it is something we are working on and aim to release later this year. VEP can report reference miss-matches for GRCh38, but these data are not available for GRCh37.</p><div style="box-sizing: border-box; margin-top: 0px; color: rgb(36, 41, 46); font-family: -apple-system, system-ui, "Segoe UI", Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; font-size: 14px; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255); margin-bottom: 0px !important;" class="">Kind Regards,</div><div style="box-sizing: border-box; margin-top: 0px; color: rgb(36, 41, 46); font-family: -apple-system, system-ui, "Segoe UI", Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; font-size: 14px; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255); margin-bottom: 0px !important;" class="">Andrew</div><div style=""><br class=""><blockquote type="cite" class=""><div class="">On 20 Jun 2018, at 10:53, Wallace Ko <<a href="mailto:myko@l3-bioinfo.com" class="">myko@l3-bioinfo.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello,<div class=""><br class=""></div><div class="">I have a variant '<font face="monospace, monospace" class="">2 31754395 . C T . . .</font>' annotated by VEP web service: <a href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?db=core;tl=5Xnr0Kx2ezfI8lj3-4292985" class="">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?db=core;tl=5Xnr0Kx2ezfI8lj3-4292985</a></div><div class=""><br class=""></div><div class="">The resulting HGVS notations are:</div><div class=""><ul class=""><li class="">HGVSc: NM_000348.3:c.679G>A<br class=""></li><li class="">HGVSp: NP_000339.2:p.Arg227Gln<br class=""></li></ul></div><div class="">Searching the HGVSp on ClinVar, a corresponding result <a href="https://www.ncbi.nlm.nih.gov/clinvar/variation/3351" class="">https://www.ncbi.nlm.nih.gov/clinvar/variation/3351</a> is found. However, the coding HGVS on ClinVar's web page is <span style="font-size:small;text-align:left;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class="">NM_000348.3:c.</span><b style="font-size:small;text-align:left;text-decoration-style:initial;text-decoration-color:initial" class="">680</b><span style="font-size:small;text-align:left;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class="">G>A.</span></div><div class=""><span style="font-size:small;text-align:left;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class=""><br class=""></span></div><div class=""><span style="font-size:small;text-align:left;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class="">Checking VEP's HGVSc on Mutalyzer's name checker (<a href="https://mutalyzer.nl/name-checker?description=NM_000348.3%3Ac.679G%3EA" class="">https://mutalyzer.nl/name-checker?description=NM_000348.3%3Ac.679G%3EA</a>), an error shows that the reference base at c.679 is C instead of G.</span></div><div class=""><br class=""></div><div class="">I wonder if the HGVSc given by VEP is correct. Thank you.</div><div class=""><br clear="all" class=""><div class=""><div class="gmail_signature"><div dir="ltr" class="">Regards,<div class="">Wallace Ko</div></div></div></div>
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