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This user has accepted no answers, answered no questions, received no bounties, and received no association bonus. They also seem (as far as I can tell) to have only edited their own questions. If any questions/answers were deleted, the rep would be removed, so that doesn't affect anything either. The only activity of this user is the asking of two questions - this and this. The former question has a score of +1/-4 and the latter a score of +0/-1. This means $(1*5) - (4*-2) - (1*-2)$ or $-5$, so in other words, since SE doesn't show negative scores, the user should have a reputation of 1. However, the user has a reputation of 4.

How did this happen?

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Summarizing comments in the interest of having an answer:

The points are determined according to the timeline of events. That is, in cases where downvotes are cast before any upvotes (or other events incurring points), those have no effect on the points. This is not altered retroactively.

Consulting the user's reputation tab confirms this; the first down-votes had no effect.

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