Variant Annotation Integrator

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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
Include the GENCODE tags (if any) associated with each transcript. No transcript status data are available for the selected gene track.
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") Select RefSeq Genes or an official GENCODE release ("Basic Gene Annotation Set from GENCODE..." or "Comprehensive Gene Annotation Set...") in the "Select Genes" section above in order to make options appear.
Conservation scores
100 vertebrates conservation by PhastCons

Define Filters

Functional role
Include variants annotated as intergenic upstream/downstream of gene in transcript already subject to nonsense-mediated decay (NMD) exon loss caused by deletion 5' or 3' UTR CDS - synonymous coding change CDS - non-synonymous (missense, stop gain/loss, frameshift etc) intron splice site or splice region exon of non-coding gene "variants" for which no alternate allele has been observed

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


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