Missing compound hets with multiple VEP consequences

[hanars]

Originally posted by @anjalijain22 in #4955 (reply in thread)

Hi @hanars, migrating to the Clickhouse backend has resolved this issue! 🎉 However, I am noticing something unexpected with one variant pair in SART1 (screenshot below). The second variant has multiple VEP consequences: splice region variant, splice polypyrimidine tract variant and intron variant. I was expecting that seqr would return this variant pair if I select any of these VEP consequences however that is not the case. This variant pair is only returned when the "Intron variant" is selected as a consequence but not when I select "splice region variant" or "splice polypyrimidine tract" . Is the "splice region variant" in blue not considered to be the primary VEP annotation?