So starting a new character in a rogue trader game and my GM has said I can start with a weapon that I thought was a good shout a best quality autogun with omniscope, motion predictor ammo selector and silencer.

What I'm questioning is if this weapon would be viable, from a fluff stand point it fits the criminal/spy/assasin feel I was going for, and I planed on getting the tox rounds to add toxic to the weapon, however I'm unsure if this is a wise choice, my other weapon is a las gauntlet with whisper-bolt discharge rate and the overcharge pack (reduces ammo by half but keeps damage the same while making the beam almost invisible and silent.)

Do you guys think this could work or should I rethink? If so any suggestions that fit the theme?

I always thought a seneschal's best weapons were other people. Similar to the way the the Vanus Temple uses information and intrigue to kill rather than direct attacks. "the cleanest kill is one that another performs in your stead with no knowledge of your incitement."

That said if you want silent weapons then take a leaf out of the assassin's books and go with a needler pistol. Even when examining the body the would is almost undetectable.

Having played a seneschal for nearly 4 years, WeedyGrot has the right of it.

It is even better if you trick your GM into allowing you to start your own Death Cult. (Sorry Vawn).

You should gather ARound you a group of seeming misfits and Other assorted Characters, all specialising in one thing or another. that way you have people to do anything that needs doing. Build an information network, actively train those people on warp voyages when your character would otherwise be doing nothing, so they can be your weapons.

Take the Inferno Pistol for when all else fails and you really need to kill a *****. Make nice with High Magos on the lathes, upgrade that through role playing and expending acquisitions.

And when that fails, befriend a Lord Inquisitor, in person, murder their greatest rival for them, steal that Lord Inquisitors fortune, ship and assets, trade it for an Executor bolt/needler pistol from the Inquisitors Handbook.

Poisons work wonders for less "hands on" assassinations. The Dark Eldar have good poisons.
Also get your Mesh Armour tailor made to look like your uniform, always wear your synskin.

Twitch Mask and cybernetic eye replacements are a must.

Okay, yeah I did plan on that (sneaky manipulator was kinda the character idea for me, especially as our ships master of whispers) however I was specifically referring to that autogun. Any good (it does have a much more sneaky and subtle feel than any of the other starting weapons, without being refined which as a penal worlder I am trying to avoid) or is it a mistake?

Well ur starting off your campaign with what is essentially a tricked-out assault rifle. That's a fairly generic baseline to build off of imho.

If you want to go the route of the stealthy assassin a sniper rifle might fit you better or a silenced Ripper Pistol.

Long range combat is not something that ever comes up in our group tbh so would a sniper rifle be a good option if you took away that advantage (I am aware that the accurate quality is quite nice) I am only starting with 40 BS (not sure if that's good or not) and with the tricked out autogun I can get a +50 to hit as long as I aim for a turn first then full auto.