Variant Annotation Integrator
 
Select Genome Assembly and Region
clade genome assembly
region to annotate

Select Variants
Your session doesn't have any custom tracks or hub tracks in pgSnp or VCF format.   
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 More Annotations (optional)
+  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")

+  Conservation scores

Define Filters
+  Functional role

Configure Output
output format:
output file:   (leave blank to keep output in browser)
file type returned:  plain text   gzip compressed (ignored if output file is blank)
This tool is for research use only. While this tool is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions.




Using the Variant Annotation Integrator
 

Introduction

The Variant Annotation Integrator (VAI) is a research tool for associating annotations from the UCSC database with your uploaded set of variant calls. It uses gene annotations to predict functional effects of variants on transcripts. For example, a variant might be located in the coding sequence of one transcript, but in the intron of an alternatively spliced transcript of the same gene; the VAI will return the predicted functional effect for each transcript. The VAI can optionally add several other types of relevant information: the dbSNP identifier if the variant is found in dbSNP, protein damage scores for missense variants from the Database of Non-synonymous Functional Predictions (dbNSFP), and conservation scores computed from multi-species alignments. The VAI can optionally filter results to retain only specific functional effect categories, variant properties and multi-species conservation status.

NOTE:
The VAI is only a research tool, meant to be used by those who have been properly trained in the interpretation of genetic data, and should never be used to make any kind of medical decision. We urge users seeking information about a personal medical or genetic condition to consult with a qualified physician for diagnosis and for answers to personal questions.


Submitting your variant calls

In order to use the VAI, you must provide variant calls in either the Personal Genome SNP (pgSnp) or VCF format. pgSnp-formatted variants may be uploaded as a Custom Track. Compressed and indexed VCF files must be on a web server (HTTP, HTTPS or FTP) and configured as Custom Tracks, or if you happen to have a Track Hub, as hub tracks.

Protein-coding gene transcript effect predictions

Any gene prediction track in the UCSC Genome Browser database or in a track hub can be selected as the VAI's source of transcript annotations for prediction of functional effects. Sequence Ontology (SO) terms are used to describe the effect of each variant on genes in terms of transcript structure as follows:

SO termdescription
intergenic_variant A sequence variant located in the intergenic region, between genes.
upstream_gene_variant A sequence variant located 5' of a gene. (VAI searches within 5,000 bases.)
downstream_gene_variant A sequence variant located 3' of a gene. (VAI searches within 5,000 bases.)
5_prime_UTR_variant A variant located in the 5' untranslated region (UTR) of a gene.
3_prime_UTR_variant A variant located in the 3' untranslated region (UTR) of a gene.
synonymous_variant A sequence variant where there is no resulting change to the encoded amino acid.
missense_variant A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.