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Table 1 Variation Classification

From: A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders

Variation Class
Class Frequency Quality Impact
I + + +
II + + -
III + - +
IV + - -
V - +/- +/-
  1. Variants are automatically classified by the pipeline to help the user in detecting causative mutations (also refer to Additional file 4). A "+" sign means that the criterion indicated in the column is satisfied. Frequency criterion: the frequency in 1000 Genomes Project, Exome Variant Server and the TIGEM Variant database (in unrelated disease groups) must be < 1%; Quality criterion: the GATK variant calling tool must assign a "PASS" value to the "filter" field and score > 50 to the Genotype Quality field. Moreover, if the variant is homozygous, the percentage of reads supporting the call must be > 80%. If the variant is heterozygous, the percentage of reads supporting the call must be > 30% and < 80%); Impact criterion: the mutation causes a gain or loss of a stop codon, a gain or loss of a splicing signal, or a frame-shift in the Open Reading Frame. Alternatively, the phylogenetic conservation must be significant (i.e. the fields LJB PhyloP Pred="C" AND LJB Gerp++>2 AND Conserved>170) and 4 out of 5 prediction algorithms indicate a damaging effect (i.e. Avsift, LJB SIFT, LJB PolyPhen2, LJB LRT, LJB Mutation Taster).