Use the base spell level in general
In general, applying a metamagic feat does not change the level of the spell. From the rules on metamagic feats (emphasis mine):
Spells modified by a metamagic feat use a spell slot higher than normal. This does not change the level of the spell, so the DC for saving throws against it does not go up.
So in general, the level of the spell is not changed by metamagic and you would use the base spell level for any effect that depends on the spell's level.
One exception to this is the Heighten Spell metamagic feat which states (emphasis mine):
A heightened spell has a higher spell level than normal (up to a maximum of 9th level). Unlike other metamagic feats, Heighten Spell actually increases the effective level of the spell that it modifies. All effects dependent on spell level (such as saving throw DCs and ability to penetrate a lesser globe of invulnerability) are calculated according to the heightened level.
So when using the Heighten spell metamagic you would actually use the heightened level to determine the Variant Bloodline Arcana's effect.
The FAQ further supports this idea:
In general, use the (normal, lower) spell level or the (higher) spell slot level, whichever is more of a disadvantage for the caster. The advantages of the metamagic feat are spelled out in the Benefits section of the feat, and the increased spell slot level is a disadvantage.
Heighten Spell is really the only metamagic feat that makes using a higher-level spell slot an advantage instead of a disadvantage.