SELECT 
  count(product_id) AS count 
FROM 
  cscart_product_features_values pfv 
WHERE 
  pfv.feature_id = 18 
  AND variant_id = 5541

Query time 0.00045

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "pfv",
      "access_type": "ref",
      "possible_keys": ["PRIMARY", "fl", "variant_id", "fpl"],
      "key": "variant_id",
      "key_length": "6",
      "used_key_parts": ["variant_id", "feature_id"],
      "ref": ["const", "const"],
      "rows": 4,
      "filtered": 100,
      "using_index": true
    }
  }
}