diff --git a/truvari/variant_record.py b/truvari/variant_record.py
index 60f717a5..db9a2ba2 100644
--- a/truvari/variant_record.py
+++ b/truvari/variant_record.py
@@ -960,6 +960,8 @@ def within_tree(self, tree):
         Extract entry and tree boundaries to call `truvari.coords_within`
         """
         qstart, qend = self.boundaries()
+        if self.chrom not in tree:
+            return False
         m_ovl = tree[self.chrom].overlap(qstart, qend)
         if len(m_ovl) != 1:
             return False