8fa777e7a626753ecf40a7471999dba3a984e272
max
  Tue Apr 21 09:21:39 2020 -0700
more clinvar improvements, refs #24850

diff --git src/hg/utils/otto/clinvar/clinvar.as src/hg/utils/otto/clinvar/clinvar.as
index 4ce0768..ebcad49 100644
--- src/hg/utils/otto/clinvar/clinvar.as
+++ src/hg/utils/otto/clinvar/clinvar.as
@@ -1,39 +1,43 @@
 table clinVarBed
 "Browser extensible data (12 fields) plus information about a ClinVar entry. _clinSignCode has these possible values: BN=benign, LB=likely benign, CF=conflicting, PG=pathogenic, LP=likely pathogenic, UC=uncertain, OT=other"
     (
     string chrom;        "Chromosome (or contig, scaffold, etc.)"
     uint   chromStart;   "Start position in chromosome"
     uint   chromEnd;     "End position in chromosome"
     string name;         "Name of item"
     uint   score;      "Score from 0-1000"
     char[1] strand;    "+ or -"
     uint thickStart;   "Start of where display should be thick (start codon)"
     uint thickEnd;     "End of where display should be thick (stop codon)"
     uint reserved;     "Used as itemRgb as of 2004-11-22"
     int blockCount;    "Number of blocks"
     int[blockCount] blockSizes; "Comma separated list of block sizes"
     int[blockCount] chromStarts; "Start positions relative to chromStart"
-    lstring origName;         "ClinVar Variation Report"
+    lstring origName;         "Link to ClinVar"
     string clinSign;         "Clinical significance"
     string reviewStatus;   "Review Status"
     string type;         "Type of Variant"
     string geneId;         "Gene Symbol"
+    string molConseq;         "Molecular Consequence"
     string snpId;         "dbSNP ID"
     string nsvId;         "dbVar ID"
     lstring rcvAcc;         "ClinVar Allele Submission"
     string testedInGtr;         "Genetic Testing Registry"
     lstring phenotypeList;         "Phenotypes"
     lstring phenotype;         "Phenotype identifiers"
-    string origin;         "Data origin"
+    string origin;         "Allele origin"
     string assembly;         "Genome assembly"
     string cytogenetic;         "Cytogenetic status"
     lstring hgvsCod;         "Nucleotide HGVS"
     lstring hgvsProt;         "Protein HGVS"
     string numSubmit;         "Number of submitters"
     string lastEval;         "Last evaluation"
     string guidelines;         "Guidelines"
     lstring otherIds;         "Other identifiers e.g. OMIM IDs, etc."
     lstring _mouseOver;        "Mouse over text"
     string _clinSignCode;        "Clinical Significance"
+    string _originCode;        "Allele Origin Code"
+    string _allTypeCode;        "Variation Type"
     uint _varLen;            "Variant Length in base pairs "
+    uint _starCount;         " number of stars "
     )