ACR RECEIVES PRE DEP CLRNC WITH ALT CHANGE FROM ASSIGNED SID. FLIES SID ALT. ALTDEV.

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FLT EWR-GSO. NEWARK 4 DEP RWY 22 -- SID CALLS FOR 5000 FT INITIAL ALT. PRE DEP CLRNC RECEIVED PRIOR TO PUSHBACK OVER ACARS COMPUTER. INITIAL ALT CHANGE -- 2500 FT. 2500 SET IN ALT ALERTER PER ACARS. DURING TAXI OUT CAPT BRIEFED DEP PROC WITH 5000 FT RESTRICTION AS PRINTED. ALT ALERTER SET TO 5000. NO ALT ADVISORIES GIVEN BY TWR ON DEP REMINDING CHANGE. TOOK OFF; CALLED DEP AT 1000 FT SAYING FLT 'OUT OF 1100 FOR 5000 FT.' DEP ACKNOWLEDGED AND GAVE HDG CHANGE. AT 3000 FT DEP CALLED ASKING ALT. FLT REPLIED 'OUT OF 3400 FOR 5000.' DEP REPLIED 'IT'S 2500 TODAY -- CONTINUE TO 10000 NOW.' NO OTHER CALL MADE CONCERNING ALT -- NO CONFLICT ON TCASII OR FROM CTLR MENTIONED. RECOMMENDATION: PRINTED SID AND 2500 FT IN THIS DIRECTION ARE IN CONFLICT. PRE DEP CLRNC OVER ACARS IS LOOKED AT BUT REPLACED WITH WT AND BAL AND TKOF DATA BEFORE TKOF. RECOMMEND EITHER LEAVING SID ALT AS PUBLISHED OR ISSUING CLRNC OTHER THAN SID. A QUICK REMINDER BY TWR ON TKOF CLRNC 'CLRED FOR TKOF; FLY NEWARK 4 MAINTAIN 2500' WOULD ELIMINATE THE PROB.