Table 2.

VAFs detected in Case #2′s glioma using a NGS panel

Gene	Transcript	Exon	Genomic	cDNA	Variant classification	Variant frequency
ATRX	NM_000489.3	Ex9	chrX:g.76939909CA>C	c.838delT	Pathogenic	0.66
IDH1	NM_005896.3	Ex4	chr2:g.209113112C>T	c.395G>A	Pathogenic	0.32
TP53	NM_000546.5	Ex5	chr17:g.7578542G>A	c.388C>T	Pathogenic	0.77

Notice the doubling of the ATRX VAF for this male patient compared to IDH1, present in an autosome. TP53 presented with loss-of-heterozygosity (LOH), which is in agreement with the observed mutation frequency being approximately double of IDH1