MySQL performance issues with occasional complete freezes
Rate Per Second = RPS
From the available (very incomplete) global status and global variables posted, please consider the following suggestions to improve performance.
innodb_log_file_size=512M  # from ~ 50M for log rotation reduction from 6 minutes to about 30 minutes.
innodb_log_buffer_size=256M  # from 16M for ~ 30 minutes RAM storage before write required
innodb_buffer-pool_size=40G  # from 12G to reduce innodb_data_reads RPS of 934
thread_cache_size=100  # from 8 to reduce threads_created count and overhead required
tmp_table_size=128M  # from 16M to expand capacity of in RAM tmp tables
max_heap_table_size=128M  # match tmp_table_size and reduce created_tmp_disk_tables RPhr of 1371

Observation, select_scan RPS of 37 indicates additional indexes would reduce table scans.
Use your slow query log and EXPLAIN SELECT xxxxx to assist with finding table and columns missing indexes.
Posting more complete data to pastebin.com would allow more complete analysis and there are many more Global Variables that could enhance speed of instance.