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Annotations

This page will describe what is displayed in scout, what the different annotations mean and how they are parsed from the vcf file.

Frequencies

1000G

The frequency from the 1000G population database.

1000G_MAX_AF

The maximum allele frequency of all populations in the 1000G population database.

ExAC

The frequency from the ExAC population database.

ExAC_MAX_AF

The maximum allele frequency of all populations ExAC population database.

Severity

CADD score

The Combined Annotation Dependent Depletion(CADD) score. A prediction of the deleterioussness for a variant.

SIFT

The SIFT) prediction for how a variation affects the protein.

PolyPhen

The PolyPhen) prediction for how a variation affects the protein.

Conservation

Gerp

The Genomic Evolutionary Rate Profiling(GERP) conservation string. An estimation of how conserved this position is.

phastCons

The PHASTcons conservation string.

phylop

The phylop 100 way predicted conservation string.

External ID

COSMIC

A matching exact CHROM, POS, REF, ALT from vcf with Catalogue Of Somatic Mutations In Cancer (COSMIC). A link to COSMIC if a matching COSMIC variant is found.