Table III.

Classification of eight novel heterozygous variants in KIT exon 11.

Location of die alteration		In silico prediction		ACMG/AMP Classification by Genetic Variant Interpretation Tool		Cancer Genome Interpreter
Nucleotide change (c .notation)	Amino ccid change (p.notation)	Align GVGD	MutadonTaster2	Criterion	Pathogenicity	Oncogenic prediction
c.l652_1672del	p.(Pro55 l_Lys558dehnsGln)	Class C65 (GV: 0.00 - GD: 75.14)	Prediction disease causing - long InDel. Model: complex_aae. prob: 0.999999999999935	PM1.PM2. PM4. PP3	Likely pathogenic (IV)	Predicted driver: tier 1
c.l653_16bOdelinsAA	p.(Met552_Ghi554delinsLys)	Class C65 (GV: 0.00 - GD: 94.49)	Prediction disease causing. Model: complex_aae. prob: 0.895033008598755	PM1.PM2. PM4. PP3	Likely pathogenic (IV)	Predicted driver: tier 1
c.l665_1672delinsCC	p.(Trp557_Lys558del)	N/A	Prediction polymorphism. Model: complex_aae. prob: 0.981440878256269	PM1.PM2. PM4	Likely pathogenic (IV)	Predicted driver: tier 2
c.l66S_16S6del	p.(Trp557')	N/A	Prediction disease causing. Model: complex_aae. prob. 1	PM1.PM2. PM4. PP3	Likely pathogenic (IV)	Predicted driver: tier 2
c.l676_1720del	p .(Val559_Thr574dehnsAla)	Class C55 (GV: 0.00 - GD: 64.43)	Prediction disease causing - long InDel. Model: complex_aae. prob: 0. 99999994804898S	PM1.PM2. PM4. PP3	Likely pathogenic (IV)	Predicted driver: tier 1
c.l715_175odup	p.(Pro5S5_Arg5Soinsl4)	N/A	Prediction polymorphism Model: complex_aae. prob: 0.999999947411599	PM1.PM2. PM4	Likely pathogenic (IV)	Predicted passenger
c,1721_1765dup	p.(Arg5S8_Leu5S9insl5)	N/A	Prediction polymorphism. Model: complex_aae. prob: 0.999999998406041	PM1.PM2. PM4	Likely pathogenic (IV)	Predicted passenger
c,1722_1766dup	p .(Gln575_Leu5 89dup)	Class C65 (GV: 0.00 - GD: 112.44)	Prediction polymorphism Model: complex_aae. prob: 0.999999998406041	PM1.PM2. PM4	Likely pathogenic (IV)	Predicted driver: tier 2

Pathogenicity was determined using ACMG/AMP criterions. N/A, not avaliable.