Book of Virtues: Spawns purple glowing rune wisps on the middle ring. The wisps spawn random Runes/Soul Stones when destroyed, and enemies killed by the wisps' tears have a 15% chance to drop a Rune/Soul Stone. A wisp is given even if Isaac is not holding a rune when the item is used.
Car Battery: Essentially uses the rune or soul stone twice.
Jera: Allows Isaac to copy pickups with every use. This combination can double Lil' Batteries, which can both circumvent the rune's high charge time and allow for game-breaking combos with repeated use of the synergy.
Void: If Void absorbs both Clear Rune and a consumable-producing item like Mom's Bottle of Pills the latter takes effect first, shifting any held rune out of the primary consumable slot and rendering the Clear Rune effect useless.
This item's unlock method is likely a nod to its similar functionality to Blank Card but Clear Rune being unable to follow the same naming convention due to Blank Rune already existing.
Despite being introduced in the Repentance DLC, Clear Rune's place in the Collection Menu is on Page 3, along with other Rebirth items. This is due to the item taking up a previously unused item id. This also means that this item needs to be unlocked and picked it up in a normal run to get both !Platinum God! and The Real Platinum God achievements.
Book of Virtues: Spawns purple glowing rune wisps on the middle ring. The wisps spawn random Runes/Soul Stones when destroyed, and enemies killed by the wisps' tears have a 15% chance to drop a Rune/Soul Stone. A wisp is given even if Isaac is not holding a rune when the item is used.
Car Battery: Essentially uses the rune or soul stone twice.
Jera: Allows Isaac to copy pickups with every use. This combination can double 
Lil' Batteries, which can both circumvent the rune's high charge time and allow for game-breaking combos with repeated use of the synergy.
Tarot Cloth: No effect.
Void: If Void absorbs both Clear Rune and a consumable-producing item like 
Mom's Bottle of Pills the latter takes effect first, shifting any held rune out of the primary consumable slot and rendering the Clear Rune effect useless.
Blank Card and 
Placebo.
Blank Rune already existing.
!Platinum God! and 
The Real Platinum God achievements.
The Binding of Isaac: Rebirth
