Databases of reported disease-causing mutations

Human Gene Mutation Database (HGMD)- http://www.hgmd.cf.ac.uk/
Online Mendelian Inheritance in Man (OMIM)- http://www.omim.org/
ClinVar- http://www.ncbi.nlm.nih.gov/clinvar/ 
DECIPHER- http://decipher.sanger.ac.uk/
Locus-specific databases- http://www.hgvs.org/dblist/glsdb.html

Databases of genetic variation

dbSNP- http://www.ncbi.nlm.nih.gov/projects/ SNP/
HapMap- http://hapmap.ncbi.nlm.nih.gov
1000 Genomes- http://www.1000genomes.org/                      
dbVar-  http://www.ncbi.nlm.nih.gov/dbvar/
DGVa- http://www.ebi.ac.uk/dgva/
DGV- http://projects.tcag.ca/variation/   
Exome Variant Server- http://evs.gs.washington.edu/EVS

Tools for annotation of sequence variants

Variant Effect Predictor (Ensembl)- http://www.ensembl.org/info/docs/ variation/vep/index.html 
Variant Annotation Tool- http://vat.gersteinlab.org/ 
ANNOVAR- http://www.openbioinformatics.org/ annovar/ 
snpEff- http://snpeff.sourceforge.net/
PolyPhen2- http://genetics.bwh.harvard.edu/pph2/ 
SIFT- http://sift.jcvi.org/
MutationTaster- http://www.mutationtaster.org/ 
PhD-SNP- http://gpcr2.biocomp.unibo.it/~emidio/PhD-SNP/PhD-SNP_Help.html 
PhyloP- http://compgen.bscb.cornell.edu/phast/index.php 
GERP- http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html 
ConDel- http://bg.upf.edu/condel/home 


Splice Prediction Algorithms:

NNSplice- http://www.fruitfly.org/seq_tools/splice.html 
NetGene2- http://www.cbs.dtu.dk/services/ NetGene2/
Human Splicing Finder- http://www.umd.be/HSF/

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