1942abfbe86d5b3f5ed3ad0482a31a9354587e18
max
  Tue Mar 26 09:30:03 2024 -0700
preparing clinvar for somatic mutations, no ticket yet

diff --git src/hg/utils/otto/clinvar/clinvarSub.sql src/hg/utils/otto/clinvar/clinvarSub.sql
new file mode 100644
index 0000000..bb3aa5c
--- /dev/null
+++ src/hg/utils/otto/clinvar/clinvarSub.sql
@@ -0,0 +1,25 @@
+# clinvarSub.sql was originally generated by the autoSql program, which also 
+# generated clinvarSub.c and clinvarSub.h.  This creates the database representation of
+# an object which can be loaded and saved from RAM in a fairly 
+# automatic way.
+
+#ClinVar variant submission info
+CREATE TABLE clinvarSub (
+    varId int not null,	# the identifier assigned by ClinVar and used to build the URL, namely https://ncbi.nlm.nih.gov/clinvar/VariationID
+    clinSign varchar(255) not null,	# interpretation of the variation-condition relationship
+    dateLastEval varchar(255) not null,	# the last date the variation-condition relationship was evaluated by this submitter
+    description longblob not null,	# an optional free text description of the basis of the interpretation
+    subPhenoInfo longblob not null,	# the name(s) or identifier(s)  submitted for the condition that was interpreted relative to the variant
+    repPhenoInfo longblob not null,	# the MedGen identifier/name combinations ClinVar uses to report the condition that was interpreted. 'na' means there is no public identifer in MedGen for the condition.
+    revStatus varchar(255) not null,	# the level of review for this submission, namely http//www.ncbi.nlm.nih.gov/clinvar/docs/variation_report/#review_status
+    collMethod varchar(255) not null,	# the method by which the submitter obtained the information provided
+    originCounts varchar(255) not null,	# origin and the number of observations for each origin
+    submitter varchar(255) not null,	# the submitter of this record
+    scv varchar(255) not null,	# the accession and current version assigned by ClinVar to the submitted interpretation of the variation-condition relationship
+    subGeneSymbol varchar(255) not null,	# the gene symbol reported in this record
+    explOfInterp longblob not null,	# more details if ClinicalSignificance is 'other' or 'drug response'
+    somClinImpact longblob not null,    #    the somatic classification of clinical impact on this submitted record
+    oncogenicity varchar(255) not null,  #  the somatic classification of oncogenicity on this submitted record
+              #Indices
+    INDEX(varId)
+);