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Variant Annotation Integrator
 
Select Genome Assembly and Region
Current Genome: Dec. 2013 (GRCh38/hg38)

region to annotate

Select Variants
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variants:
maximum number of variants to be processed:
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Select Genes
The gene predictions selected here will be used to determine the effect of each variant on genes, for example intronic, missense, splice site, intergenic etc.


Select Regulatory Annotations
The annotations in this section provide predicted regulatory regions based on various experimental data. When a variant overlaps an annotation selected here, the consequence term regulatory_region_variant will be assigned. Follow the links to description pages that explain how each dataset was constructed. Some datasets cover a significant portion of the genome and it may be desirable to filter these annotations by cell type and/or score in order to avoid an overabundance of hits.
DNase I Hypersensitivity Peak Clusters from ENCODE (95 cell types)
+  filter items

Select More Annotations (optional)
-  Database of Non-synonymous Functional Predictions (dbNSFP)
dbNSFP (Liu et al. 2015) release 3.1a provides pre-computed scores and predictions of functional significance from a variety of tools. Every possible coding change to transcripts in Gencode release 22 (Ensembl 79, Mar. 2015) gene predictions has been evaluated. Note: This may not encompass all transcripts in your selected gene set.

Variant Effect Scoring Tool (VEST) (scores [0-1] predict confidence that a change is deleterious
SIFT (D = damaging, T = tolerated)
PolyPhen-2 with HumDiv training set (D = probably damaging, P = possibly damaging, B = benign)
PolyPhen-2 with HumVar training set (D = probably damaging, P = possibly damaging, B = benign)
MutationTaster (A = disease causing automatic, D = disease causing, N = polymorphism, P = polymorphism automatic)
MutationAssessor (high or medium: predicted functional; low or neutral: predicted non-functional)
Likelihood ratio test (LRT) (D = deleterious, N = Neutral, U = unknown)
InterPro protein domains
GERP++ Rejected Substitutions (RS)
GERP++ Neutral Rate (NR)

+  Transcript status
-  HGVS variant nomenclature
The Human Genome Variation Society (HGVS) has established a sequence variant nomenclature, an international standard used to report variation in genomic, transcript and protein sequences.
Include HGVS genomic (g.) terms in output
Include HGVS coding (c.) terms if applicable, otherwise noncoding (n.) terms, in output
Include HGVS protein (p.) terms (if applicable) in output
When including HGVS protein (p.) terms, add parentheses around changes to emphasize that they are predictions
For variants that involve both a deletion and insertion, including multi-nucleotide variants, include the deleted sequence (e.g. show "delAGinsTT" instead of only "delinsTT")

-  Known variation
Include dbSNP rs# ID if one exists

+  Conserved elements
+  Conservation scores

Define Filters
+  Functional role