GET-Evidence: Qualifiers

Qualifiers

Qualifiers are added to this to describe the variant evidence and clinical importance of a variant, these qualifiers are automatically generated from the variant impact score. An example of how qualifiers are attached to variant impact (in this case “pathogenic”) follows:

low evidence moderate evidence high evidence
low importance low clinical importance,
uncertain pathogenic
low clinical importance,
likely pathogenic
low clinical importance,
pathogenic
moderate importance moderate clinical importance,
uncertain pathogenic
moderate clinical importance,
likely pathogenic
moderate clinical importance,
pathogenic
high importance high clinical importance,
uncertain pathogenic
high clinical importance,
likely pathogenic
high clinical importance,
pathogenic

Insufficiently evaluated qualifier

A variant is considered insufficiently evaluated if not enough scoring fields have been filled in. To be considered sufficiently evaluated a variant must have:

  1. At least one of either “case/control” or “familial” evidence categories filled in
  2. The “severity” and “penetrance” categories in clinical importance categories filled in. (Not necessary for benign or protective variants.)

Variant evidence qualifier

The variant evidence qualifier is determined according to the following:

  • “high evidence”:
    1. least 4 points in either “Case/control evidence” or “Familial evidence”
    2. and at least eight points total in evidence categories
  • “moderate evidence”:
    1. at least 3 points in either “Case/control evidence” or “Familial evidence”
    2. and at least five stars total in evidence categories
  • “low evidence”: Any variants which do not meet the above requirements

Clinical importance qualifier

Clinical importance is determined according to the following rules:

  • “high clinical importance”:
    1. At least 4 points in penetrance (high-moderate penetrance / >= 20% attributable risk)
    2. and either:
      1. At least 3 stars in severity and at least 4 stars in treatability
      2. or at least 4 stars in severity
  • moderate clinical importance”:
    1. At least 3 points in penetrance (moderate penetrance / >= 5% attributable risk)
    2. and either:
      1. At least 2 stars in severity and at least 3 stars in treatability
      2. or at least 3 stars in severity
  • “low clinical importance”: Any variants which do not meet the above requirements

Gene search

"GENE" or "GENE A123C":

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