Question: Non Coding, Synonymous Snp Prediction Tool ?
gravatar for Radhouane Aniba
9.7 years ago by
Radhouane Aniba760 wrote:

Hi all,

I am trying to list all predictive tool that are able to predict : NON-CODING, SYNONYMOUS SNPs that are putatively causing disease.

Have you an idea on such tools names (with website if possible)

I have in my list

ANNOVAR ENSEMBL variation API (snp effect predictor tool) SNPnexus is-rSNP

Any idea is welcome



disease snp • 4.6k views
ADD COMMENTlink modified 9.5 years ago by Pierre Lindenbaum133k • written 9.7 years ago by Radhouane Aniba760

What is your input data ? rsIDs (known SNPs) or nucleotide positions (novel SNPs from sequencing) ?

ADD REPLYlink written 9.7 years ago by Khader Shameer18k
gravatar for Pierre Lindenbaum
9.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

This question has already been answered on biostar:

however, I would like to cite this new database: dbNSFP ( )

The dbNSFP is an integrated database of functional predictions from multiple algorithms for the comprehensive collection of human non-synonymous SNPs (NSs). Its current version (ver 1.0) is based on CCDS version 20090327 and includes a total of 75,931,005 NSs. It compiles prediction scores from four prediction algorithms (SIFT, Polyphen2, LRT and MutationTaster), a conservation score (PhyloP) and other related information.

ADD COMMENTlink modified 16 months ago by _r_am32k • written 9.7 years ago by Pierre Lindenbaum133k

Not sure i understand this comment - you can see on the screenshot ( that it predicts all the consequences of a SNP that can currently be done reliably (i.e. it can say that a snp is synonymous or non synonymous but doesn't predict if the SNP is in something like an miRNA which is harder to delineate)

ADD REPLYlink written 9.7 years ago by Pi520

So in sum only snpEff is able to predict Synonymous SNPs ? no other predictors ? I am browsing the litterature actually it is hard to fine a paper clearly mentionning that.


ADD REPLYlink written 9.7 years ago by Radhouane Aniba760
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