Table 1. The count of all variants, and completely novel variants in each functional effect group separated by allele frequency categories.

Variant consequence annotations	All variants	Singletons	Doubletons	MAF⩽0.01	0.01<MAF⩽0.02	0.02<MAF⩽0.05	0.05<MAF⩽0.1	MAF>0.1
All variants
Loss_of_function	1775	892	219	100	152	93	79	240
Non_synonymous	60  011	22 939	6988	3626	6119	4834	3944	11 561
Splice_region	8748	2657	886	468	892	791	689	2365
Synonymous	44 582	12 891	4292	2501	4491	4111	3658	12 638
UTR	17 165	4945	1792	1073	1865	1585	1438	4467
ncRNA	23 033	6292	2210	1256	2274	2190	2145	6666
Intronic	131 531	35 463	13  016	7519	13 797	12 426	11 828	37 482
Upstream	2056	506	206	118	204	181	209	632
Downstream	1142	265	108	63	105	114	131	356
Regulatory	73	13	8	5	8	5	11	23
Intergenic	461	106	28	18	43	38	50	178
Total	290 577	86 969	29 753	16 747	29 950	26 368	24 182	76 608
Completely novel variants
Loss_of_function	269	230	27	7	5	0	0	0
Non_synonymous	4783	3978	515	167	116	3	1	3
Splice_region	552	455	60	17	19	1	0	0
Synonymous	2141	1738	250	85	57	5	1	5
UTR	1702	1312	240	81	59	5	0	5
ncRNA	2273	1772	305	109	71	8	3	5
Intronic	13  308	10  328	1890	604	427	30	11	18
Upstream	230	175	32	7	9	1	0	6
Downstream	120	86	19	8	6	0	0	1
Regulatory	9	6	3	0	0	0	0	0
Intergenic	44	38	3	2	0	1	0	0
Total	25 431	20 118	3344	1087	769	54	16	43