3aac12402e976f74beef84827e0602ba7cc1cc58
mspeir
  Mon Nov 29 12:42:33 2021 -0800
Fixing filters for clinvar SNV track, refs #28562

diff --git src/hg/makeDb/trackDb/human/trackDb.clinvar.ra src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
index 91d1d48..e5065da 100644
--- src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
+++ src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
@@ -8,31 +8,31 @@
 noParentConfig on
 itemRgb on
 urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/"
 scoreLabel ClinVar Star-Rating (0-4)
 
         track clinvarMain
         parent clinvar
         shortLabel ClinVar SNVs
         longLabel ClinVar Short Variants < 50bp
         visibility hide
         group phenDis
         itemRgb on
         priority 1
         type bigBed 12 +
         showCfg on
-        filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,UC|uncertain,OT|other,VUS|vus
+        filterValues._clinSignCode B|benign,LB|likely benign,CF|conflicting,P|pathogenic,LP|likely pathogenic,RF|risk factor,OT|other,VUS|vus
         filterType._clinSignCode multiple
         filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,UNK|unknown
         filterType._originCode multiple
         filterLabel._originCode Alelle Origin
         filterValues._allTypeCode SNV|single nucleotide variant - SNV,INS|insertion - INS,DEL|deletion - DEL,INDEL|insertion-deletion - INDEL,dupl|duplication - DUPL,OTH|other - OTH
         filterType._allTypeCode multiple
         filter._varLen 0
         filterByRange._varLen on
         filterLimits._varLen 0:49
         filterValues.molConseq genic downstream transcript variant|genic downstream transcript variant,no sequence alteration|no sequence alteration,inframe indel|inframe indel,stop lost|stop lost,genic upstream transcript variant|genic upstream transcript variant,initiatior codon variant|initiatior codon variant,inframe insertion|inframe insertion,inframe deletion|inframe deletion,splice acceptor variant|splice acceptor variant,splice donor variant|splice donor variant,5 prime UTR variant|5 prime UTR variant,nonsense|nonsense,non-coding transcript variant|non-coding transcript variant,3 prime UTR variant|3 prime UTR variant,frameshift variant|frameshift variant,intron variant|intron variant,synonymous variant|synonymous variant,missense variant|missense variant,|unknown
         mouseOverField _mouseOver
         bigDataUrl /gbdb/$D/bbi/clinvar/clinvarMain.bb
         urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/"
         noScoreFilter on
         searchIndex _dbVarSsvId