diff --git a/compiler/src/dotty/tools/dotc/core/TypeComparer.scala b/compiler/src/dotty/tools/dotc/core/TypeComparer.scala
index a0eb5139eb07..cf2507aa1724 100644
--- a/compiler/src/dotty/tools/dotc/core/TypeComparer.scala
+++ b/compiler/src/dotty/tools/dotc/core/TypeComparer.scala
@@ -1338,8 +1338,11 @@ class TypeComparer(@constructorOnly initctx: Context) extends ConstraintHandling
             }
           } || tryLiftedToThis2
 
-        case _: TypeVar =>
-          recur(tp1, tp2.superType)
+        case tv: TypeVar =>
+          if tv.isInstantiated then
+            recur(tp1, tp2.superType)
+          else
+            compareAppliedType2(tp2, tv.origin, args2)
         case tycon2: AnnotatedType if !tycon2.isRefining =>
           recur(tp1, tp2.superType)
         case tycon2: AppliedType =>
diff --git a/tests/pos/i12478.scala b/tests/pos/i12478.scala
new file mode 100644
index 000000000000..d1e247ae4e68
--- /dev/null
+++ b/tests/pos/i12478.scala
@@ -0,0 +1,19 @@
+sealed trait Foo[T]
+
+object Foo:
+  case class Bar[F[_]](fu: List[F[Unit]]) extends Foo[F[Unit]]
+
+class Test:
+  def id1[T1](foo1: Foo[T1]): Foo[T1] = foo1 match
+    case Foo.Bar(fu) =>
+      Foo.Bar(fu)
+
+  def id2[T2](foo2: Foo[T2]): Foo[T2] = foo2 match
+    case bar2 @ (_: Foo.Bar[f]) =>
+      val fu2 = bar2.fu
+      Foo.Bar(fu2)
+
+  def id3[T3](foo3: Foo[T3]): Foo[T3] = foo3 match
+    case bar3 @ Foo.Bar(_) =>
+      val fu3 = bar3.fu
+      Foo.Bar(fu3)