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/lib/bigDbSnp.c src/hg/lib/bigDbSnp.c
index 863d8af..8ebf546 100644
--- src/hg/lib/bigDbSnp.c
+++ src/hg/lib/bigDbSnp.c
@@ -301,53 +301,65 @@
 struct symbolDesc
 {
     char *symbol;
     char *description;
 };
 
 struct symbolDesc ucscNotesDesc[] =
     {
     { bdsAltIsAmbiguous,
       "At least one alternate allele "
       "contains an IUPAC ambiguous base (e.g. 'R' for 'A or G')." },
     { bdsClassMismatch,
       "Variation class/type is inconsistent with alleles mapped to this genome assembly." },
     { bdsClinvar,
       "Variant is in ClinVar." },
+    { bdsClinvarBenign,
+      "Variant is in ClinVar with clinical significance of benign and/or likely benign." },
+    { bdsClinvarConflicting,
+      "Variant is in ClinVar with reports of both benign and pathogenic significance." },
+    { bdsClinvarPathogenic,
+      "Variant is in ClinVar with clinical significance of pathogenic and/or likely pathogenic." },
     { bdsClusterError,
       "This variant has the same start, end and class as another variant; "
       "they probably should have been merged into one variant." },
     { bdsCommonAll,
       "Variant is \"common\", i.e. has a Minor Allele Frequency of at least 1% "
       "in all projects reporting frequencies." },
     { bdsCommonSome,
       "Variant is \"common\", i.e. has a Minor Allele Frequency of at least 1% "
       "in some, but not all, projects reporting frequencies." },
     { bdsDiffMajor,
       "Different frequency sources have different major alleles "
       "(see table of allele frequencies above)." },
     { bdsFreqIsAmbiguous,
       "At least one allele reported by at least one project "
       "contains an IUPAC ambiguous base (e.g. 'R' for 'A or G')." },
     { bdsFreqNotRefAlt,
       "The reference genome allele is not the major allele in at least one project." },
     { bdsMultiMap,
       "This variant has been mapped to more than one distinct genomic location." },
     { bdsOverlapDiffClass,
       "This variant overlaps another variant with a different type/class." },
     { bdsOverlapSameClass,
       "This variant overlaps another with the same type/class but different start/end." },
+    { bdsRareAll,
+      "Variant is \"rare\", i.e. has a Minor Allele Frequency of less than 1% "
+      "in all projects reporting frequencies, or has been reported without frequency data." },
+    { bdsRareSome,
+      "Variant is \"rare\", i.e. has a Minor Allele Frequency of less than 1% "
+      "in some, but not all, projects reporting frequencies." },
     { bdsRefIsAmbiguous,
       "The reference genome allele "
       "contains an IUPAC ambiguous base (e.g. 'R' for 'A or G')." },
     { bdsRefIsMinor,
       "The reference genome allele is not the major allele in at least one project." },
     { bdsRefIsRare,
       "The reference genome allele is rare (i.e. allele frequency < 1%)." },
     { bdsRefIsSingleton,
       "The reference genome allele has never been observed "
       "in a population sequencing project reporting frequencies." },
     { bdsRefMismatch,
       "The reference genome allele reported by dbSNP differs from the GenBank assembly sequence." },
     { bdsRevStrand,
       "The orientation of the currently viewed reference genome sequence is different from "
       "the orientation of dbSNP's preferred assembly; alleles are "