SELECT 
  product_id, 
  group_id 
FROM 
  cscart_product_variation_group_products 
WHERE 
  group_id IN (559, 561, 556)

Query time 0.00061

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "3.91"
    },
    "table": {
      "table_name": "cscart_product_variation_group_products",
      "access_type": "range",
      "possible_keys": [
        "idx_group_id"
      ],
      "key": "idx_group_id",
      "used_key_parts": [
        "group_id"
      ],
      "key_length": "3",
      "rows_examined_per_scan": 7,
      "rows_produced_per_join": 7,
      "filtered": "100.00",
      "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_variation_group_products`.`group_id` in (559,561,556))",
      "cost_info": {
        "read_cost": "3.21",
        "eval_cost": "0.70",
        "prefix_cost": "3.91",
        "data_read_per_join": "112"
      },
      "used_columns": [
        "product_id",
        "group_id"
      ]
    }
  }
}