Challenges imposed by minor reference alleles on the identification and reporting of clinical variants from exome data

Table 2 Variants with disease-associated reference alleles in thrombophilia genes

Gene	Variant	Minor Allele Frequency			Reference alleles		Disease allele	ClinVar variants
Gene	Variant	1000G	ExAC	Allele	hg19	hg38	Disease allele	ClinVar variants
F5	rs6025	0.0060	0.0215	T	T	C	A	c.1601G > A, c.1601G=
F13B	rs6003	0.2382	0.1280	C	C	C	G	c.344G > A
PLAU	rs2227564	0.2246	0.2454	T	T	T	T	c.371C > T
NOS3	rs1799983	0.1763	0.2470	T	T	T	T	c.894 T > G

ISSN: 1471-2164