bihealth / auto-acmg

Automatic classification of sequence variants and CNVs according to ACMG criteria.
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Implement `PS4` criteria #108

Closed gromdimon closed 3 months ago

gromdimon commented 5 months ago

Is your feature request related to a problem? Please describe. Impelemtn this criteria

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Additional context

PS4

PS4 (prevalence)

No automation has been implemented.

Original Definition

The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls

Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0. See manuscript for detailed guidance.

Note 2: In instances of very rare variants where case-control studies may not reach statistical significance, the prior observation of the variant in multiple unrelated patients with the same phenotype, and its absence in controls, may be used as moderate level of evidence.

-- Richards et al. (2015); Table 4
gromdimon commented 3 months ago

Due to data restrictions, this criteria cannot be implemented for now. -> Archiving