acca3deffc05c4d8d11590a1cf3d893763254712
angie
  Thu Oct 31 13:43:05 2019 -0700
dbSnp153: Adding new ucscNotes suggested by Ana Benet: clinvar{Benign,Conflicting,Pathogenic}, rareAll, rareSome.  refs #23283

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 03ba3fb..4cb2458 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -1617,31 +1617,31 @@
 priority 6.8
 
 track dbSnp153Composite
 compositeTrack on
 shortLabel dbSNP 153
 longLabel Short Genetic Variants from dbSNP release 153
 detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp153Details.tab.gz
 group varRep
 visibility pack
 url https://www.ncbi.nlm.nih.gov/snp/$$
 urlLabel dbSNP: 
 type bigDbSnp
 freqSourceOrder 1000Genomes,GnomAD_exomes,TOPMED,ExAC,PAGE_STUDY,GnomAD,GoESP,Estonian,ALSPAC,TWINSUK,NorthernSweden,Vietnamese
 classFilterValues snv,mnv,ins,del,delins,identity
 classFilterType multipleListOr
-ucscNotesFilterValues |(nothing noted),classMismatch|Variant class/type is inconsistent with allele sizes,clinvar|Present in ClinVar,clusterError|Overlaps a variant with the same type/class and position,commonAll|MAF >= 1% in all projects that report frequencies,commonSome|MAF >= 1% in at least one project that reports frequencies,delMismatch|Deleted sequence mismatches genomic reference sequence,diffMajor|Different projects report different major alleles,multiMap|Variant is placed in more than one genomic position,overlapDiffClass|Variant overlaps other variant(s) of different type/class,overlapSameClass|Variant overlaps other variant(s) of same type/class but different position,refIsMinor|Genomic reference allele is minor allele in at least one project that reports frequencies,refIsRare|Genomic reference allele frequency is <1% in at least one project,refIsSingleton|Genomic reference frequency is 0 in all projects reporting frequencies,revStrand|Variant maps to opposite strand relative to dbSNP's preferred top-level placement
+ucscNotesFilterValues |(nothing noted),classMismatch|Variant class/type is inconsistent with allele sizes,clinvar|Present in ClinVar,clinVarBenign|ClinVar significance of benign and/or likely benign,clinvarConflicting|Clinvar includes both benign and pathogenic reports,clinvarPathogenic|ClinVar significance of pathogenic and/or likely pathogenic,clusterError|Overlaps a variant with the same type/class and position,commonAll|MAF >= 1% in all projects that report frequencies,commonSome|MAF >= 1% in at least one project that reports frequencies,delMismatch|Deleted sequence mismatches genomic reference sequence,diffMajor|Different projects report different major alleles,multiMap|Variant is placed in more than one genomic position,overlapDiffClass|Variant overlaps other variant(s) of different type/class,overlapSameClass|Variant overlaps other variant(s) of same type/class but different position,refIsMinor|Genomic reference allele is minor allele in at least one project that reports frequencies,refIsRare|Genomic reference allele frequency is <1% in at least one project,refIsSingleton|Genomic reference frequency is 0 in all projects reporting frequencies,revStrand|Variant maps to opposite strand relative to dbSNP's preferred top-level placement
 #'
 ucscNotesFilterType multipleListOr
 maxFuncImpactFilterValues 0|(not annotated),0865|frameshift,1587|stop_gained,1574|splice_acceptor_variant,1575|splice_donor_variant,1821|inframe_insertion,1583|missense_variant,1590|terminator_codon_variant,1819|synonymous_variant,1580|coding_sequence_variant,1623|5_prime_UTR_variant,1624|3_prime_UTR_variant,1619|nc_transcript_variant,2153|genic_upstream_transcript_variant,1986|upstream_transcript_variant,2152|genic_downstream_transcript_variant,1987|downstream_transcript_variant,1627|intron_variant
 maxFuncImpactFilterType multipleListOr
 priority 0.8
 
     track dbSnp153Common
     parent dbSnp153Composite on
     shortLabel Common dbSNP (153)
     longLabel Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 153
     bigDataUrl /gbdb/$D/snp/dbSnp153Common.bb
     priority 1
 
     track dbSnp153ClinVar
     parent dbSnp153Composite