SELECT 
  product_id, 
  group_id 
FROM 
  cscart_product_variation_group_products 
WHERE 
  group_id IN (54, 49, 25, 51)

Query time 0.00019

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "cscart_product_variation_group_products",
      "access_type": "range",
      "possible_keys": ["idx_group_id"],
      "key": "idx_group_id",
      "key_length": "3",
      "used_key_parts": ["group_id"],
      "rows": 12,
      "filtered": 100,
      "index_condition": "cscart_product_variation_group_products.group_id in (54,49,25,51)"
    }
  }
}