#!/bin/bash
s='IID,kgp11004425,rs11274005,kgp183005,rs746410036,kgp7979600
1,00,AG,GT,AK,00
32,AG,GG,AA,00,AT
100,TT,AA,00,AG,AA       
3,GG,AG,00,GT,GG'

sed -E '1!{:a;s~^([^,]*,.*)00~\1N/A~;ta;}' <<< "$s"