SELECT 
  product_id, 
  group_id 
FROM 
  cscart_product_variation_group_products 
WHERE 
  group_id IN (
    54, 49, 25, 51, 19, 50, 55, 48, 35, 13, 32, 
    27
  )

Query time 0.00030

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "cscart_product_variation_group_products",
      "access_type": "index",
      "possible_keys": ["idx_group_id"],
      "key": "PRIMARY",
      "key_length": "6",
      "used_key_parts": ["product_id", "group_id"],
      "rows": 126,
      "filtered": 34.12698364,
      "attached_condition": "cscart_product_variation_group_products.group_id in (54,49,25,51,19,50,55,48,35,13,32,27)",
      "using_index": true
    }
  }
}