Table 2.

Candidate variants in six families with hereditary diffuse gastric cancer without CDH1 pathogenic variants

	Number of sequenced individuals	Gene	Variant	Consequence	Protein change	Minimum allele frequency		SIFT	Polymorphism Phenotyping
						1000 Genomes European sample	ExAC non-TCGA European sample
4	3	PALB2	c.757-758TAG→T	Frameshift deletion	Leu253fs	0	0	NA	NA
6	1	RECQL5	c.2806-2T→C	Splice-acceptor variant	NA	0	0	NA	NA
8	1	MSH2	c.967-968T→TCTCA	Frameshift insertion	Ser323fs	0	0	NA	NA
11	5	ATR	c.6075A→T	Stop site gain	Tyr2025X	0	0	NA	NA
11	5	NBN	c.1124+1G→C	Splice-donor variant	NA	0	0	NA	NA
12	1	MSH2	c.1A→C	Start site loss	Met1?*	0	0	Deleterious	Benign
21	2	RECQL5	c.2828C→T	Missense variant	Arg943His	0·002	0·014332	Deleterious	Probably damaging

SIFT=Sorting Intolerant From Tolerant. ExAC=Exome Aggregation Consortium. TCGA=The Cancer Genome Atlas. fs=frameshift. NA=not applicable.

^*Human Genome Variation Society nomenclature to indicate loss of a start site without experimental evidence of a new start site.²⁰