diff --git a/src/cljam/io/vcf/util/validator.clj b/src/cljam/io/vcf/util/validator.clj
index 63747e3a..28138141 100644
--- a/src/cljam/io/vcf/util/validator.clj
+++ b/src/cljam/io/vcf/util/validator.clj
@@ -47,15 +47,16 @@
      (constantly false))
    entry))
 
-(defn- check-entry [entry {:keys [type number]}]
+(defn- check-entry [entry {:keys [type number]} alt-num]
   (let [entries (if (and (= number 1) (not (sequential? entry)))
                   [entry] entry)
         type-check (and entry
                         (not (every? #(check-entry-type
                                        % type) entries)))
-        number-check (not (or (= number "A")
-                              (not entry)
-                              (= (count entries) number)))]
+        number' (cond (= number "A") alt-num
+                      :else number)
+        number-check (not (or (nil? entry)
+                              (= (count entries) number')))]
     (when (or type-check number-check)
       (cond
         type-check
@@ -74,7 +75,7 @@
          [id entry] (get variant sample)
          :let [fmt (get mformat id)
                res (if fmt
-                     (check-entry entry fmt)
+                     (check-entry entry fmt (count (:alt variant)))
                      (format "key %s not in meta." id))]
          :when res]
      [[sample id] res])))
diff --git a/test/cljam/io/vcf/util/validator_test.clj b/test/cljam/io/vcf/util/validator_test.clj
index 2ab42436..a8efd04d 100644
--- a/test/cljam/io/vcf/util/validator_test.clj
+++ b/test/cljam/io/vcf/util/validator_test.clj
@@ -35,7 +35,7 @@
           {:A {:type "Integer" :number 2}})))
     (is (not
          (#'validator/check-each-samples
-          {:normal {:A [1 2]}} [:normal]
+          {:normal {:A [1 2]} :alt ["A"]} [:normal]
           {:A {:type "Integer" :number "A"}})))
     (is (string?
          (get-in