Свидетельница молчала не потому, что боялась, а потому, что хотела сначала подумать.

Свидетельница means female witness.
Russian often marks biological sex in nouns referring to people, so:

• свидетель = witness (usually male, or sometimes generic in some contexts)
• свидетельница = female witness

In this sentence, the speaker is clearly referring to a woman.

Because the subject свидетельница is feminine singular, and Russian past tense verbs agree with gender and number.

Compare:

• он молчал = he was silent / he kept quiet
• она молчала = she was silent / she kept quiet
• они молчали = they were silent / kept quiet

So свидетельница молчала means the female witness was silent / kept silent.

Молчать means to be silent, to keep quiet, or not to speak.

So свидетельница молчала does not just describe a character trait like she was a quiet person. It means that in that situation, she did not say anything.

This is a very common Russian pattern meaning:

• not because ..., but because ...

So:

• не потому, что боялась = not because she was afraid
• а потому, что хотела сначала подумать = but because she wanted to think first

It is a set contrastive structure. English learners can think of it as a direct equivalent of not because X, but because Y.

In this structure, а is the natural choice.

Russian often uses а when contrasting two explanations, especially in patterns like:

• не ..., а ...
• не потому, что ..., а потому, что ...

Here а sets up a correction or contrast:

• not this reason,
• but that reason.

Но can also express contrast, but in this exact pattern а потому, что is the standard form.

The commas are there because the sentence contains subordinate clauses introduced by что and also a contrastive structure.

Breakdown:

• Свидетельница молчала,
• не потому, что боялась,
• а потому, что хотела сначала подумать.

Why the commas:

1. что боялась is a subordinate clause.
2. что хотела сначала подумать is another subordinate clause.
3. The two parts are contrasted with а.

So the punctuation is normal and expected.

Good question. In many sentences, потому что works as a conjunction meaning because.

For example:

• Она молчала, потому что боялась.
  = She was silent because she was afraid.

But in this sentence, the structure is не потому, что ..., а потому, что .... In that pattern, Russian treats the sentence as a correlative construction, and потому is separated from что by the logic of the larger sentence.

So yes, learners often first meet потому что as a single because, but here it appears inside a bigger pattern:
not because ..., but because ...

Russian often leaves that unstated if the meaning is general or obvious from context.

So боялась can simply mean:

• was afraid
• felt scared

If you want to say what she was afraid of, Russian can add it:

• боялась его = was afraid of him
• боялась говорить = was afraid to speak
• боялась, что ошибётся = was afraid that she would make a mistake

Here the object is omitted because the sentence only needs the general idea she was afraid.

Yes. Хотеть is commonly followed by an infinitive:

• хотела подумать = wanted to think
• хотела сказать = wanted to say
• хотела уйти = wanted to leave

So this is completely normal Russian grammar:

• хотела = wanted
• подумать = to think

This is about verbal aspect.

• думать = imperfective, focusing on the process of thinking
• подумать = perfective, often meaning to think for a while / to think something over / to give it some thought

In this sentence, хотела сначала подумать suggests:

• she wanted to think first,
• then presumably speak or act afterward.

So подумать fits well because it presents the thinking as a bounded, purposeful action before the next step.

If you said хотела сначала думать, it would sound less natural here, because the point is not the ongoing process in general, but to stop and think first.

Сначала means first, at first, or before doing anything else.

Here it means:

• she wanted to think first

In other words, she was silent because she wanted to reflect before speaking.

So the sentence implies a sequence:

1. first think,
2. then speak or react.

That placement is very natural in Russian. It directly modifies the infinitive:

• хотела сначала подумать = wanted first to think / wanted to think first

Russian word order is flexible, so other versions are possible depending on emphasis, for example:

• хотела подумать сначала

But хотела сначала подумать is the most neutral and natural phrasing here.

Inside this sentence, it is understood as part of the fixed pattern не потому, что ..., а потому, что ..., so the meaning is clearly causal:

• not because she was afraid, but because...

By itself, что often means that, but after потому in this construction it introduces the reason clause.

So here you should not translate что боялась separately as that she was afraid. The whole chunk потому, что боялась functions as because she was afraid.

Yes. A simpler version would be:

• Свидетельница молчала не из-за страха, а потому, что хотела сначала подумать.

Or even:

• Свидетельница молчала не из-за того, что боялась, а из-за того, что хотела сначала подумать.

But the original sentence is very natural and elegant.
Не потому, что ..., а потому, что ... is a common and polished way to contrast two reasons.