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Last active August 29, 2015 13:57
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Discrepancies in PolyPhen2 predictions.
Raw
summary.md

Example

Nonsynonymous change in question (human, build 37; 1-based coordinate)
chrom: chr22 
pos:   24379402
ref:   T
alt:   G

Ensembl VEP (from website)

Transcripts with non-synymous changes: ENST00000248935, ENST00000436103
Polyphen2 scores for those transcripts: 0.534, 0.828

Ensembl VEP (command line utility)

Transcripts with non-synymous changes: ENST00000248935, ENST00000436103
Polyphen2 scores for those transcripts: 0.865, 0.797

dbNSFP 2.4

Transcripts with non-synymous changes: ENST00000248935, ENST00000436103
Polyphen2 scores for those transcripts: Only reports a single score for HDIV (0.961) and HVAR(0.736)

**I gather the single score is meant to reflect that it applies to both transcripts?**
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