I recommend you use Ensembl VEP. Among other many relevant things to catalog a variant as damaging, you will get CLIN_SIG or ClinVar significance classifier. Using VEP's web interface for small jobs will work just fine. For larger jobs and for more customizable usage you can install it locally. Not hard if you go the Ensembl virtual machine route.
Do you want to do analysis of Clinvar data, or do you want to annotate your own data with Clinvar and analyze that? Your question doesn't make that clear but I am assuming you want to do the later, as just parsing through the Clinvar VCF for pathogenic variants doesn't require much. If you want to annotate your own VCFs with Clinvar data I would suggest a few options. As @Carlos Borroto suggests you can use VEP. You could also use GEMINI, which will add ClinVar annotations to VCF files that are already annotated with VEP or with snpEff and convert it into a database (sqlite3 by default but moving to support with SQL-based database backends) which you can then query and explore. If you just want to add ClinVar annotations to your VCF directly, and then query the VCF itself however you like there is also VCFAnno, which is a fast annotator of VCFs based on any listed VCFs or BED files as you choose. It is fast, powerful, and flexible and basically accomplishes a lot of what GEMINI does without converting to a database at the end. I am now using a combination of snpEff and VCFAnno to add custom annotations to my VCF files, I am then storing my variants in a Cassandra database.
you meant you want to insert this into Apache Hive and you need some Hive insert statements ?
what do you want to query ? how is it different from inserting it in Hive ?
Yes, insert this into Apache Hive.
I wanted to know if using Hive is an option or is there a better way of doing this?
it depends your needs / what you want to query.
I want to identify pathological variants