Interpreting dbNSFP prediction scores
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2.7 years ago
greeness ▴ 20

How should I interpret for example, SIFT score:

SIFT_pred = T;T;T;T;D;T
SIFT_score = 0.138;0.138;0.138;0.138;0.042;0.157

From dbNSFP documentation, I understand the meaning of D and T

  • D: Deleterious (sift<=0.05);
  • T: tolerated (sift>0.05)

My question is: Why there are multiple values of both pred and score in this example?

dbNSFP VEP SIFT • 1000 views
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Entering edit mode

Hello greeness,

just a quick guess about this. AFAIK the prediction depends on the transcript, as SIFT need to know whether the variant is located in an exon, intron, ... and if there is an amino acid change. So I guess these multiple values are for different transcripts.

Where did you get this value from?

fin swimmer

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Entering edit mode
2.7 years ago
greeness ▴ 20

I guess I found the answer from dbNSFP readme file:

January 23, 2014: dbNSFP v2.2 is released. SIFT and FATHMM now have multiple scores corresponding to different Ensembl ENSP ids and amino acid positions (aapos_SIFT and aapos_FATHMM). Accordingly, our companion search program now supports SNP searches based on Ensembl ENSP ids and amino acid positions.

So each value corresponds to different Ensembl ENSP id and amino acid position (aapos_SIFT and aapos_FATHMM).

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