SELECT 
  product_id, 
  group_id 
FROM 
  cscart_product_variation_group_products 
WHERE 
  group_id IN (39, 35, 40)

Query time 0.00026

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.005704015,
    "nested_loop": [
      {
        "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"],
          "loops": 1,
          "rows": 11,
          "cost": 0.005704015,
          "filtered": 100,
          "attached_condition": "cscart_product_variation_group_products.group_id in (39,35,40)",
          "using_index": true
        }
      }
    ]
  }
}