Table 1.

Computational/in silico tools for annotation and characterization of genomic variants

Variant Type	Tool	Description	Citation
Coding	Ensembl	Predicting effect of variant/amino acid substitution	[14]
	Meta-SNP		[92]
	PANTHER		[93]
	PolyPhen-2		[87]
	PredictSNP 2.0		[8,90]
	PROVEAN		[88]
	SIFT		[86]
	SNPs&GO		[89]
	SNPsnap		[94]
	SuSPect		[96]
	UMD-Predictor		[95]
	NetSurf2.0	Surface accessibility effects	[97]
	SOPMA	Secondary structure effects	[98]
	I-mutant-3.0	Protein stability effects	[99]
	ConSurf	Evolutionary conservation	[100]
	HOPE	3D structure effects	[101]
	SWISS-MODEL	Homology modeling	[102]
Promoter/Enhancer	MotifBreakR	TFBS disruption	[117]
	RegulomeDB	Regulatory DNA variant prediction	[108]
	Basenji	Deep learning	[123]
	DeepSea		[121]
	COLOC	Colocalization	[124]
	eCaviar		[25]
	FUSION		[127]
	MetaXcan		[125,126]
Splicing	GeneSplicer	Splicing site and variant effect prediction	[131]
	Human Splicing Finder		[130]
	NetGene2		[132,133]
	RegSNPs-intron		[128]
	SpliceAI		[129]
5’/3’ UTRs	ExUTR	3’ UTR sequence prediction	[111]
	RegulomeDB	UTR variant effect prediction	[108]
	UTRannotator	5’ UTR variant effect prediction	[112]
	UTRscan	UTR sequence prediction	[109,110]
miRNA/lncRNA	CPSS 2.0	miRNA and lncRNA sequence prediction	[116]
	MicroSNiPer	miRNA variant effect prediction	[115]
	miR2GO		[114]
	SubmiRine		[113]