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Sefer in biblical Hebrew means any kind of "book" or written document (plural s'farim). It is derived from the same Hebrew root-word as sofer ("scribe"), sifriyah ("library") and safrut ("literature").
Among Orthodox Jews the word is used for books both of the Tanakh, the oral law (Mishnah and Talmud) or any work of Rabbinic literature. Works unrelated to Torah study are rarely called sefer by English-speaking Orthodox Jews. Among Hebrew-speaking Ashkenazi Jews, the differentiation between books related to Torah study and other books is made by referring to the former with traditional Ashkenazi pronunciation (SEY-fur) and to the latter with Modern Hebrew pronunciation (SEF-fer).
The word sefer contains in it the same root as the one used for Mispar, which means a number.