diff --git a/deeprvat/data/dense_gt.py b/deeprvat/data/dense_gt.py
index 16670651..bfe93c5c 100644
--- a/deeprvat/data/dense_gt.py
+++ b/deeprvat/data/dense_gt.py
@@ -73,6 +73,7 @@ def __init__(
         genes_to_keep: Optional[Set[str]] = None,
         gene_file: Optional[str] = None,
         gene_types_to_keep: Optional[List[str]] = None,
+        exclude_variant_cols: List[str] = [],
         ignore_by_annotation: Optional[List[Tuple[str, Any]]] = None,
         max_pval: Optional[Dict[str, float]] = None,
         variants: Optional[pd.DataFrame] = None,
@@ -185,7 +186,9 @@ def __init__(
         )
 
         self.transform_data()
-        self.setup_variants(min_common_variant_count, min_common_af, variants)
+        self.setup_variants(
+            min_common_variant_count, min_common_af, variants, exclude_variant_cols
+        )
 
         self.get_variant_metadata(grouping_level)
 
@@ -479,6 +482,7 @@ def setup_variants(
         min_common_variant_count: Optional[int],
         min_common_af: Optional[Dict[str, float]],
         train_variants: Optional[pd.DataFrame],
+        exclude_variant_cols: List[str],
     ):
         logger.debug("Setting up variants")
         if min_common_variant_count is None and min_common_af is None:
diff --git a/dnanexus/config.yaml b/dnanexus/config.yaml
index d140044c..7a5f5e4b 100644
--- a/dnanexus/config.yaml
+++ b/dnanexus/config.yaml
@@ -43,7 +43,7 @@ model:
 
 data:
     gt_file: /mnt/project/DeepRVAT/DeepRVAT/data/preprocessed/genotypes.h5
-    variant_file: /mnt/project/DeepRVAT/DeepRVAT/data/variants.parquet
+    variant_file: /mnt/project/DeepRVAT/DeepRVAT/data/variants_90pct10dp_qc.parquet
     dataset_config:
         min_common_af:
             MAF: 0.01
@@ -110,6 +110,8 @@ data:
             - DeepRipe_plus_QKI_parclip
             - SpliceAI_delta_score
         gene_file: /mnt/project/DeepRVAT/DeepRVAT/data/protein_coding_genes.parquet
+        exclude_variant_cols:
+            - 90pct10dp_qc
         use_common_variants: False
         use_rare_variants: True
         rare_embedding: