Sequence ontology (SO) allows to standardize terminology used for assessing sequence changes and impact. This allows for a common language across all variant annotation programs and makes it easier to communicate using a uniform terminology. Starting from version 4.0 VCF output uses SO terms by default. See below for the location of each display term relative to the transcript structure:
The terms in the table below are shown in order of severity (more severe to less severe) as estimated by SnpEff.
|SO Term||SO Description||SO Accession|
The ESP is a NHLBI funded exome sequencing project aiming to identify genetic variants in exonic regions from over 6000 individuals, including healthy ones as well as subjects with different diseases. The variant call data set is constantly being updated. As the size of the database is more than 1000 Genomes Project and the fold coverage is far higher, this data set will be particularly useful for users with exome sequencing data sets. As of October 2012, esp5400 and esp6500 are available, representing summary statistics from 5400 exomes and 6500 exomes, respectively. As of February 2013, the most recent version of ESP is esp6500si, so whenever possible, users should use this database for annotation. Compared to esp6500, the esp6500si contains more calls, and indel calls and chrY calls.
SIFT( S orting I ntolerant F orm T olerant) predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. The data provide for each amino acid substitution is a score and a qualitative prediction (either ’tolerated’ or ’deleterious’). The score is the normalized probability that the amino acid change is tolerated so scores nearer to 0 are more likely to be deleterious. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called ’deleterious’ and all others are called ’tolerated’.
Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm Nature Protocols 4(8):1073-1081 (2009)doi:10.1038/nprot.2009.86
ClinVar is a freely accessible, data archive of reports of the relationships among human variations and phenotypes hosted by the National Center for Biotechnology Information (NCBI) and funded by intramural National Institutes of Health (NIH) funding.
The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.http://gnomad.broadinstitute.org
The *_SNP_indel_ANNO.xlsx file contains information about variants found at specific positions in the reference genome. Each data line contains information about a single variant.
Each column of the file has the following meaning.