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Advanced options provides a means to specify aspects of the annotation generated from the VEP annotation task.  Upon invoking the task dialog, Option set is set to Default.  Clicking Configure will open a window to specify additional components of annotation (Figure 2).  VEP has Advanced options for Identifiers, Output options, and Co-located variants.  Moving the mouse cursor over the info button  will provide details for each parameter.

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In the report, there variant impact information, it is a subjective classification of the severity of the variant consequence:

Low: a variant that is assumed to be mostly harmless or unlikely to change protein behavior

Moderate: a non-disruptive variant that might change protein effectiveness

Modifier: usually non-coding variants or variants affecting non-coding genes, where predictions are difficult or there is no evidence of impact

High: a variant is assumed to have high disruptive impact in the protein, probably causing protein truncation, loss of function or triggering nonsense mediated decay.

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