Table 1.

Rare associations annotated in ClinVar database

CHR	POS	Ref/Alt	Gene	MAF	Trait	Effect	SE	P-value	Clinvar var. ID	Protein change	Molecular consequence	Condition	Class
1	55,523,798	A/G	PCSK9	0.0032	LDL	−0.2933	0.0364	7.26E-16	630597	I424V	Missense	Familial hypercholesterolemias	Benign
					TC	−0.2642	0.0358	1.69E-13
1	155,261,697	G/A	PKLR	0.0055	TG	0.1489	0.0277	7.58E-08	292806	R490W	Missense	Pyruvate kinase deficiency of red cells	Uncertain significance
1	155,263,025	A/G	PKLR	0.0019	HbA1c	−0.4154	0.074	1.97E-08	225440	V460A	Missense	Pyruvate kinase deficiency of red cells	Uncertain significance
2	21,228,437	A/G	APOB	0.001	LDL	−0.8857	0.0657	1.97E-41	630249	I3768T	Missense	Familial hypercholesterolemias	Uncertain significance
					TC	−0.7885	0.0651	1.00E-33
2	44,050,063	G/A	ABCG5	0.0012	LDL	0.4076	0.0594	6.80E-12	30485	R446*	Nonsense	Sitosterolemia	Pathogenic
					TC	0.3758	0.0588	1.63E-10
2	44,100,999	A/G	ABCG8	0.0074	LDL	0.1784	0.0241	1.25E-13	499929	M429V	Missense	–	Uncertain significance
					TC	0.1518	0.0238	1.81E-10
2	44,116,923	C/T	LRPPRC	0.0091	LDL	0.1261	0.0217	6.07E-09	746339	A1360T	Missense	–	Benign
9	107,560,803	C/T	ABCA1	0.0076	HDL	−0.1447	0.0235	7.50E-10	364396	V1674I	Missense	Tangier disease, Familial High Density Lipoprotein Deficiency	Benign
					TC	−0.1317	0.0235	2.14E-08
9	107,584,945	C/A	ABCA1	0.0061	HDL	−0.2315	0.0266	3.64E-18	225290	C887F	Missense	Familial hypercholesterolemia 1	Uncertain significance
					TC	−0.1815	0.0265	7.96E-12
10	101,165,607	T/C	GPT	0.0032	AST	−0.2246	0.04	1.90E-08	709106	E183G	Missense	–	Benign
11	116,701,560	G/A	APOC3	0.0008	HDL	0.8077	0.0755	1.02E-26	139561	A43T	Missense	Apolipoprotein C-III deficiency, Coronary heart disease	Pathogenic
					TG	−0.8409	0.0761	2.39E-28
11	116,703,580	A/G	APOC3	0.0017	TG	−0.3203	0.0492	7.73E-11	17902	T74A	Missense	Apolipoprotein c-iii, nonglycosylated	Pathogenic
15	43,507,389	C/T	EPB42	0.0028	HbA1c	−0.3386	0.0587	7.88E-09	13233	A142T	Missense	Spherocytosis type 5	Pathogenic
16	56,917,997	C/T	SLC12A3	0.0022	HDL	0.2593	0.0443	4.97E-09	225468	A569V	Missense	Familial hypokalemia-hypomagnesemia	Uncertain significance
16	56,918,023	G/A	SLC12A3	0.0047	HDL	−0.1608	0.0297	5.91E-08	225469	V578M	Missense	Familial hypokalemia-hypomagnesemia	Benign
16	57,016,150	G/A	CETP	0.0005	HDL	1.3379	0.0877	1.60E-52	17524	-	Splice donor	Hyperalphalipoproteinemia 1	Pathogenic
17	41,246,724	C/T	BRCA1	0.0023	TG	0.3234	0.0429	4.72E-14	55726	G275D	Missense	Breast-ovarian cancer, familial 1, Hereditary cancer-predisposing syndrome, Neoplasm of the breast, AllHighlyPenetrant	Benign
19	11,217,315	C/T	LDLR	0.0002	LDL	1.0777	0.1429	4.59E-14	251446	R257W	Missense	Familial hypercholesterolemia	Conflicting interpretation
					TC	0.9784	0.1374	1.07E-12
19	11,227,576	C/T	LDLR	0.0002	LDL	1.5104	0.1428	3.80E-26	200921	H583Y	Missense	Familial hypercholesterolemia	Conflicting interpretation
					TC	1.2383	0.1428	4.29E-18
19	11,241,988	C/T	LDLR	0.0014	LDL	−0.3384	0.0607	2.49E-08	374957	A860V	Missense	Familial hypercholesterolemia	Benign
19	45,207,444	C/T	CEACAM16	0.009	LDL	−0.1694	0.0219	1.02E-14	226509	S180F	Missense	–	Benign
20	43,042,364	C/T	HNF4A	0.0084	HDL	−0.1451	0.0228	2.07E-10	129240	T114I	Missense	Maturity onset diabetes mellitus in young, Hyperinsulinism, Mongenic diabetes	Benign

Chromosomal positions are based hg19. Effect size is based on alternative allele. ClinVar database was assessed at 1st May 2020. From the conditional analysis results, attenuated rare variants are bold-faced.

CHR chromosome, POS position, MAF minor allele frequency.