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TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
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Schaefer-2014-POLR1D #416

Closed pnrobinson closed 5 years ago

pnrobinson commented 5 years ago

For this disease, the correct gene is found but there is a homozygous variant that is judged to be non-pathogenic (score 0.716). This brings down the total prob a lot.

Q<D:Microretrognathia[HP:0000308]<Micrognathia[HP:0000347][74.854]: E:Downslanted palpebral fissures[HP:0000494][28.118]: D<Q:Conductive hearing impairment[HP:0000405]<Hearing impairment[HP:0000365][9.254]: Q~D:Malar flattening[HP:0000272]~Abnormality of facial skeleton[HP:0011821][0.010]

There is an option in lines 387-389 (comment out), but this reduced the rank from 111 to 145. Todo -- try this on the entire cohort and decide what the best option is.

There is probablty no realistic way of getting the rank for this case better since the variant gets such a bad score.

pnrobinson commented 5 years ago

We are as good as it gets right now. Closing.