SELECT 
  product_id, 
  feature_id, 
  variant_id 
FROM 
  cscart_product_features_values 
WHERE 
  product_id IN (
    12999, 12998, 12997, 12996, 12995, 12994, 
    12993, 12992, 12991, 12990, 12989, 
    12988
  ) 
  AND feature_id IN (
    646, 647, 595, 628, 627, 624, 625, 553, 
    626, 622, 623, 636, 637
  ) 
  AND lang_code = 'en'

Query time 0.00523

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "10.01"
    },
    "table": {
      "table_name": "cscart_product_features_values",
      "access_type": "range",
      "possible_keys": [
        "PRIMARY",
        "fl",
        "lang_code",
        "product_id",
        "fpl",
        "idx_product_feature_variant_id"
      ],
      "key": "PRIMARY",
      "used_key_parts": [
        "feature_id",
        "product_id",
        "variant_id",
        "lang_code"
      ],
      "key_length": "15",
      "rows_examined_per_scan": 28,
      "rows_produced_per_join": 28,
      "filtered": "100.00",
      "using_index_for_skip_scan": true,
      "cost_info": {
        "read_cost": "7.21",
        "eval_cost": "2.80",
        "prefix_cost": "10.01",
        "data_read_per_join": "21K"
      },
      "used_columns": [
        "feature_id",
        "product_id",
        "variant_id",
        "lang_code"
      ],
      "attached_condition": "((`test2_gaseus`.`cscart_product_features_values`.`product_id` in (12999,12998,12997,12996,12995,12994,12993,12992,12991,12990,12989,12988)) and (`test2_gaseus`.`cscart_product_features_values`.`feature_id` in (646,647,595,628,627,624,625,553,626,622,623,636,637)) and (`test2_gaseus`.`cscart_product_features_values`.`lang_code` = 'en'))"
    }
  }
}