Table 2.

Variants classified as VUS by at least one interpreter. In total 27 variants’ interpretations showed discordance between BIs and CGs.

Variant ID	Gene	Transcript	Genomic Location	HGVS	Nucleotide Exchange	Amino Acid Exchange	Variant Type	rs Code ClinVar ID	Evidence Coded by BI_1	Evidence Coded by BI_2	Evidence Coded by CG_1	Evidence Coded by CG_2	Final BI_1 Report	Final BI_2 Report	Final CG_1 Report	Final CG_2 Report
14	APC	NM_000038.6	chr5:112175211	NC_000005.9:g.112175211 T > A	c.3920 T > A	p.(Ile1307Lys)	Ms	rs1801155 822	PS3, PM2, PP5, BP1	BP1, BP4	BS1, BS2	BS1, BS2	LP	LP	VUS	VUS
15	BRCA1	NM_007294.4	chr17:41243451	NC_000017.10:g.41243451 C > T	c.4096 + 1 G > A	-	Spl	rs80358178 37565	PVS1, PM2	PVS1, PM2, PP3	PM2, PP3	PVS1, PM2, PP3	LP	P	VUS	P
16	CHEK2	NM_007194.4	chr22:29120962	NC_000022.10:g.29120962 T > A	c.592 + 3 A > T	-	SNV/ Spl**	rs587782849 142956	PS3, PM2	PVS1-M, PM2	PM2	PM2	LP	VUS	VUS	VUS
20	MSH2	NM_000251.2	chr2:47637348	NC_000002.11:g.47637348 T > C	c.482 T > C	p.(Val161Ala)	Ms	rs63750126 565544	PM1, PM2, PM5, PP3, BP1	PM2, PM5, PP3, BP1	PM2, PM5, PP3	PM2, PM5, PP3	LP	VUS	P	P
22	CHEK2	NM_007194.4	chr22:29121058	NC_000022.10:g.29121058 C > T	c.499 G > A	p.(Gly167Arg)	Ms	rs72552322 142524	PS3, PM1, PM2, PP3	PM2, BP1, PP3, PP5	PM2, PP5	PM2, PP3, PP5	LP	VUS	P	LP
25	BRCA1	NM_007294.4	chr17:41209088	NC_000017.10:g.41209088 C > G	c.5258 G > C	p.(Arg1774Thr)	Ms	rs397509246 55488	PS3, PM1, PM2, PP3, BP1	PM2, BP1, PP3, PP5	PM2, PP5	PS3, PM2, PP3, PP5	LP	VUS	P	P
37	MUTYH	NM_001128425.2	chr1:45798559	NC_000001.10:g.45798559_45798571del	c.504 + 19_504 + 31del	-	Intronic	rs781222233 406825	PM2, PP1, PP5	PM2, PP5	PM2, PP5	PM2, PP5	LP	VUS	LP	LP
45	MLH1	NM_000249.3	chr3: 37059093	NC_000003.11:g.37059093 A > C	c.884 + 3 A > C	-	Spl	rs267607803 90413	PM2, PP3, PP5	PVS1-M, PM2	PM2	PM2	LP	VUS	VUS	VUS
48	BRCA2	NM_000059.4	chr13:32954050	NC_000013.10:g.32954050 G > A	c.9117 G > A	p.(Pro3039 = )	Syn	rs28897756 38215	PVS1, PS3, PM2, PP3, PP5	PS3-M, PM2, PP5	PP5, PM2	PP5, PM2	P	VUS	P	P
49	CHEK2	NM_007194.4	chr22:29090054	NC_000022.10:g.29090054 G > A	c.1427 C > T	p.(Thr476Met)	Ms	rs142763740 128060	PM1, PP3, BS1	PP3, BP1	PM1, PM2, PM5, PP3, PP5, BP1	PM2, PM5, PP5	VUS	VUS	P	LP
50	MUTYH	NM_001128425.1	chr1:45796890	NC_000001.10:g.45796891_45796893del	c.1437_1439del	p.(Glu480del)	Fs	rs587778541 127838	PM2, PM4, PS3, PP5	PM2, PP5	PM2, PM4, PS3, PP5	PM2, PM4, PS3, PP5	VUS	P	P	P
51	ATM	NM_000051.3	chr11:108186590	NC_000011.9:g.108186590 A > G	c.6047 A > G	p.(Asp2016Gly)	Ms	rs587781302 140823	PM2, PP3, PP5, BP1	PM2, PP5, PP3	PM2, PP5, PP3	PM2, PP3, PP5	VUS	LP	LP	LP
52	ATM	NM_000051.3	chr11:108186638	NC_000011.9:g.108186638 G > A	c.6095 G > A	p.(Arg2032Lys)	Ms	rs139770721 181974	PM2, PP3, PP5, BP1	PM2, PP5	PM2, PP5	PM2, PP3, PP5	VUS	LP	LP	LP
53	TP53	NM_000546.6	chr17:7577114	NC_000017.10:g.7577114 C > T	c.824 G > A	p.(Cys275Tyr)	Ms	rs863224451 215997	PM2, PP3, PP5	PM1, PP2, PM2, PM5, PP3, PP5	PM1, PP2, PM2, PM5, PP3, PP5	PM1, PP2, PM2, PM5, PP3, PP5	VUS	P	P	P
54	ATM	NM_000051.3	chr11:108115727	NC_000011.9:g.108115727 C > T	c.875 C > T	p.(Pro292Leu)	Ms	rs747727055 229794	PM2, PP3, BP1	PM2, PP5, PP3, PP2	PM2, PP5, PP3, PP2	PM2, PP5, PP3	VUS	LP	LP	P
55	BRIP1	NM_032043.3	chr17:59885825	NC_000017.10:g.59885825_59885826delCA	c.918 + 2_918 + 3del	-	Spl	- SUB10324299	PM2	PVS1, PM2	PVS1, PM2	PVS1, PM2	VUS	LP	LP	LP

P pathogenic, LP likely pathogenic, SNV single nucleotide variation, BI bioinformatician, CG clinical geneticist, Fs frameshift, Ins insertion, Ms missense, Spl splice site, Ns nonsense, Syn synonymous, SNV single nucleotide variant.

**The variation is predicted to affect the splice site by human mutation finder tool [10].