На столе лежит шифр.

Because на can mean either on or onto, depending on the case.

• на столе = on the table (location, no movement)
• на стол = onto the table (motion toward the surface)

Here the sentence describes where something already is, so Russian uses the prepositional case: стол → столе.

Лежит is the 3rd person singular of лежать, meaning to lie or to be lying.

Russian often uses a position verb where English would often just say is. So instead of simply saying The cipher is on the table, Russian naturally says something more like The cipher is lying on the table.

This suggests the object is resting on the surface, probably flat or simply placed there.

In Russian, the verb to be is usually omitted in the present tense.

So:

• Он дома = He is at home
• Книга на столе = The book is on the table

In your sentence, there is already a main verb, лежит, so there is no need for есть.

Also, есть is not usually the normal equivalent of English is in sentences like this. If you said На столе есть шифр, it would mean something more like There is a cipher on the table, focusing on existence rather than position.

Because шифр is the subject of the sentence, and subjects are normally in the nominative case.

Here:

• На столе = location
• лежит = verb
• шифр = the thing that is lying there

So шифр stays in its dictionary form.

Both are grammatical, but they sound a little different.

• На столе лежит шифр puts the location first and often introduces new information: On the table lies a cipher / There is a cipher on the table.
• Шифр лежит на столе starts with the subject and feels more like The cipher is lying on the table.

Russian word order is flexible, and changing it often changes emphasis rather than core meaning.

Often yes, but not always as strictly as in English.

Russian commonly uses three basic position verbs:

• лежать = to lie
• стоять = to stand
• висеть = to hang

For something resting on a surface, лежать is very common. It usually suggests that the object is placed there rather than upright.

So шифр лежит на столе sounds natural if the cipher is a written note, document, paper, or something similar lying on the table.

Because на means on, while в means in.

• на столе = on the table
• в столе = in the desk / inside the table

So if something is on top of the table surface, Russian uses на.

The stress is:

• на столе́
• лежи́т
• шифр

A rough pronunciation guide:

na stuh-LYE lye-ZHEET shifr

A few notes:

• столе́ has stress on the last syllable.
• лежи́т also has stress on the last syllable.
• шифр is one syllable.

No. Russian has no articles.

So шифр can mean:

• a cipher
• the cipher

The exact meaning depends on context. Russian speakers understand this from the situation, word order, and surrounding sentences.

Sometimes Russian does allow very short verbless sentences, but here На столе лежит шифр is more complete and natural.

If you remove лежит, the sentence becomes much more compressed and context-dependent. Using лежит clearly tells you that the cipher is physically resting on the table.