diff --git a/hail/src/main/scala/is/hail/expr/ir/ExtractIntervalFilters.scala b/hail/src/main/scala/is/hail/expr/ir/ExtractIntervalFilters.scala
index 77280de352c..eed29b756cb 100644
--- a/hail/src/main/scala/is/hail/expr/ir/ExtractIntervalFilters.scala
+++ b/hail/src/main/scala/is/hail/expr/ir/ExtractIntervalFilters.scala
@@ -633,22 +633,27 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) {
     }
 
     private def compareWithConstant(l: Any, r: Value, op: ComparisonOp[_], keySet: KeySet)
-      : BoolValue = {
-      if (op.strict && l == null) return BoolValue.allNA(keySet)
-      r match {
+      : BoolValue =
+      if (op.strict && l == null) BoolValue.allNA(keySet)
+      else r match {
         case r: KeyField if r.idx == 0 =>
           // simple key comparison
           BoolValue.fromComparison(l, op).restrict(keySet)
         case Contig(rgStr) =>
-          // locus contig comparison
-          assert(op.isInstanceOf[EQ])
+          // locus contig equality comparison
           val b = getIntervalFromContig(l.asInstanceOf[String], ctx.getReference(rgStr)) match {
             case Some(i) =>
-              BoolValue(
+              val b = BoolValue(
                 KeySet(i),
                 KeySet(Interval(negInf, i.left), Interval(i.right, endpoint(null, -1))),
                 KeySet(Interval(endpoint(null, -1), posInf)),
               )
+
+              op match {
+                case _: EQ => b
+                case _: NEQ => BoolValue.not(b)
+                case _ => BoolValue.top(keySet)
+              }
             case None =>
               BoolValue(
                 KeySetLattice.bottom,
@@ -671,7 +676,6 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) {
           BoolValue.fromComparisonKeyPrefix(l.asInstanceOf[Row], op).restrict(keySet)
         case _ => BoolValue.top(keySet)
       }
-    }
 
     private def opIsSupported(op: ComparisonOp[_]): Boolean = op match {
       case _: EQ | _: NEQ | _: LTEQ | _: LT | _: GTEQ | _: GT | _: EQWithNA | _: NEQWithNA => true
diff --git a/hail/src/test/scala/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala b/hail/src/test/scala/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala
index 7a820f67253..12a76d10bda 100644
--- a/hail/src/test/scala/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala
+++ b/hail/src/test/scala/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala
@@ -497,6 +497,10 @@ class ExtractIntervalFiltersSuite extends HailSuite { outer =>
 
     checkAll(ir1, ref, ref, testRows, trueIntervals, falseIntervals, naIntervals)
     checkAll(ir2, ref, ref, testRows, trueIntervals, falseIntervals, naIntervals)
+
+    val ir3 = neq(Str("chr2"), invoke("contig", TString, k))
+    checkAll(ir3, ref, ref, testRows, falseIntervals, trueIntervals, naIntervals)
+    checkAll(not(ir1), ref, ref, testRows, falseIntervals, trueIntervals, naIntervals)
   }
 
   @Test def testLocusPositionComparison(): Unit = {