Use in clinical context
Most phenotypes are not caused by a single genetic variant but several genetic variants, often combined with environmental effects. For example, in the case of type 2 diabetes, there are many known risk factors for developing the disease, with obesity being a large contributing factor, but not everyone who is overweight will develop diabetes. It is likely that, along with such environmental risk factors, there are disease-modifying variants that predispose, or protect individuals from diseases.
Other disease-modifying variants alter the presentation of a disease/condition. This may alter the severity of presentation (even including not developing the condition at all) or include/remove particular symptoms. This may make it more difficult to diagnose some diseases and conditions, or to establish inheritance patterns.