Table 2. Simulated Multiple Nucleotide Variants within the HNF4A gene as annotated by GATK best practices.

Variant	Wild-type codon	Variant codon	GATK best practices annotation 1	GATK best practices annotation 2	Correct annotation	Likely implication for diagnostic testing ‡
1	CTG	TTC	c.838C>T p.Leu280Leu	c.840G>C p.Leu280Leu	c.838_840delinsTTC p.Leu280Phe	False negative result
2	TAA	TGG	p.*396*	p.*396*	p.*396Trpext*26	False negative result
3	TCC	AGC	c.1066T>A p.Ser356Thr	c.1067C>G p.Ser356Cys	c.1066_1067delinsAG p.Ser356Ser	False positive result
4	TCT	TGA	c.1262C>G p.Ser421Cys	c.1263T>A p.Ser421Ser	c.1262_1263delinsGA p.Ser421*	False negative result
5	AAG	AGT	c.1274A>G p.Lys425Arg	c.1275G>T p.Lys425Asn	c.1274_1275delinsGT p.Lys425Ser	False positive or negative result

‡Based on testing for dominant acting heterozygous, pathogenic loss of function variants.