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variants missing?",{"type":432,"tag":433,"props":694,"children":695},{},[696],{"type":437,"value":697},"Currently only coding and splice-related variants in disease-related genes make it to the medaling process.\nIntergenic, intronic, and UTR variants are excluded, as are those in non-coding transcripts.",{"type":432,"tag":439,"props":699,"children":701},{"id":700},"why-does-the-exac-allele-frequency-shown-differ-from-the-exac-portal",[702],{"type":437,"value":703},"Why does the ExAC allele frequency shown differ from the ExAC portal?",{"type":432,"tag":433,"props":705,"children":706},{},[707],{"type":437,"value":708},"The reported ExAC frequency may differ for several reasons:",{"type":432,"tag":540,"props":710,"children":711},{},[712,717],{"type":432,"tag":466,"props":713,"children":714},{},[715],{"type":437,"value":716},"PIE uses the TCGA-subtracted distribution of ExAC rather than the main distribution.",{"type":432,"tag":466,"props":718,"children":719},{},[720,722,729],{"type":437,"value":721},"PIE reports the primary allele frequencies in the ExAC database, specifically the AC, AN, and AF fields from the VCF distribution.\nThe ",{"type":432,"tag":472,"props":723,"children":726},{"href":724,"rel":725},"http://exac.broadinstitute.org/",[476],[727],{"type":437,"value":728},"ExAC portal",{"type":437,"value":730}," appears to use the \"adjusted\" frequencies which may be different.",{"type":432,"tag":433,"props":732,"children":733},{},[734,736,742],{"type":437,"value":735},"If you have any questions not covered here, feel free to email us at ",{"type":432,"tag":472,"props":737,"children":739},{"href":738},"mailto:support@stjude.cloud",[740],{"type":437,"value":741},"support@stjude.cloud",{"type":437,"value":481},{"title":424,"searchDepth":744,"depth":744,"links":745},2,[746,747,748,749,750,751,752,753,754],{"id":441,"depth":744,"text":444},{"id":452,"depth":744,"text":455},{"id":595,"depth":744,"text":598},{"id":606,"depth":744,"text":609},{"id":622,"depth":744,"text":625},{"id":653,"depth":744,"text":656},{"id":669,"depth":744,"text":672},{"id":689,"depth":744,"text":692},{"id":700,"depth":744,"text":703},"markdown","content:4.pecan:5.pecan-pie:2.faq.md","content","4.pecan/5.pecan-pie/2.faq.md","4.pecan/5.pecan-pie/2.faq","md",[762,764],{"_path":187,"title":763,"description":424},"Pecan PIE",{"_path":192,"title":195,"description":765},"A running changelog for the PeCan project.",1791243639408]