There are tools like ANNOVAR, SnpEff, and VEP that are widely used for variant annotation. Most variant filtration/prioritization software work on the output from these three main software. Appended below is a list of software that one can use to do variant annotation, filtration, and even prioritization.
NOTE: However you can use these free platforms in a clinical setting, they are designed for research use. In some cases, there is a clinical version available which is not free.
1- wANNOVAR: is a webtool for variant annotation, filtration, prioritization by Phenolyzer . This is an online version of the ANNOVAR .
2- GENEYX formerly known as TGex is a webtool for variant annotation by SnpEff, filtration, and prioritization (by VarElect)
3- VarAFT is a tool for variant annotation by ANNOVAR, filtration, and prioritization
4- SeattleSeq Annotation: is a webtool for ariant annotation.
5- Mendel,MD!: is a webtool for variant annotation, filtration and prioritization (?).
6- UCSC Variant Annotation Integrator
7- BrowseVCF: a web-application to quickly prioritize disease-causative variants in VCF files
8- Varsome: this is a variant classifiers based on ACMG2015
9- InterVar: variant classifiers
Annotate the variants and then filter them accordingly. You can try SnpEff and SnpSift in combination.