The one that has been around for as long as I can remember is Database of Genomic Variants. I recall there being criticism of it years ago, but I am sure that they have refined the database multiple times since then as large scale sequencing projects have concluded and methods improved.

You could try the Genome In A Bottle reference SV calls v0.6. They are for the HG002 (NA24385 PGP Ashkenazim Jewish Son) genome so shouldn't contain any rare pathogenic CNVs/SVs, but should have common SVs across the genome ("Healthy " germline copy number variation).

ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6

Quite a few groups have called CNVs/ SVs on the UK Biobank genotyping data from microarrays. Not sure if this is public yet (one of our local collaborators has a set), but a number of papers have been published off this data. This would be SVs for around 500,000 mainly healthy UK participants. When the Exome / Genome sequencing is complete on this cohort there should be a great resource for healthy CNVs.

Not directly related but an example of how a group involved in Cancer research is proposing to use the UK Biobank data. https://www.ukbiobank.ac.uk/2018/11/identification-of-functional-germline-variants-in-childhood-cancers/?platform=hootsuite