diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeCalculator.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeCalculator.java
index d480327d1e..b0b94e3c39 100644
--- a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeCalculator.java
+++ b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeCalculator.java
@@ -32,6 +32,7 @@
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.opencb.biodata.models.variant.avro.VariantType;
 
 import java.util.*;
 
@@ -73,7 +74,9 @@ protected void parseQueryParam(QueryOptions queryOptions) {
     }
 
     protected int getStart(int extraPadding) {
-        if (imprecise && variant.getSv() != null) {
+        if (imprecise && VariantType.CNV.equals(variant.getType())) {
+            return variant.getStart() - extraPadding;
+        } else if (imprecise && variant.getSv() != null) {
             return variant.getSv().getCiStartLeft() != null ? variant.getSv().getCiStartLeft() - extraPadding
                     : variant.getStart();
         } else {
@@ -83,7 +86,9 @@ protected int getStart(int extraPadding) {
     }
 
     protected int getEnd(int extraPadding) {
-        if (imprecise && variant.getSv() != null) {
+        if (imprecise && VariantType.CNV.equals(variant.getType())) {
+            return variant.getEnd() + extraPadding;
+        } else if (imprecise && variant.getSv() != null) {
             return variant.getSv().getCiEndRight() != null ? variant.getSv().getCiEndRight() + extraPadding
                     : variant.getEnd();
         } else {
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeGenericRegionCalculator.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeGenericRegionCalculator.java
index c591c84283..a5fa04fa03 100644
--- a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeGenericRegionCalculator.java
+++ b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeGenericRegionCalculator.java
@@ -20,6 +20,7 @@
 import org.opencb.biodata.models.core.Gene;
 import org.opencb.biodata.models.core.Transcript;
 import org.opencb.biodata.models.variant.Variant;
+import org.opencb.biodata.models.variant.avro.VariantType;
 import org.opencb.biodata.models.variant.avro.ConsequenceType;
 import org.opencb.biodata.models.variant.avro.ExonOverlap;
 import org.opencb.cellbase.core.ParamConstants;
@@ -43,8 +44,9 @@ public List<ConsequenceType> run(Variant inputVariant, List<Gene> geneList, bool
         parseQueryParam(queryOptions);
         List<ConsequenceType> consequenceTypeList = new ArrayList<>();
         variant = inputVariant;
-        variantEnd = getEnd(svExtraPadding);
-        variantStart = getStart(svExtraPadding);
+        int extraPadding = VariantType.CNV.equals(variant.getType()) ? cnvExtraPadding : svExtraPadding;
+        variantEnd = getEnd(extraPadding);
+        variantStart = getStart(extraPadding);
 //        isBigDeletion = ((variantEnd - variantStart) > BIG_VARIANT_SIZE_THRESHOLD);
         boolean isIntergenic = true;
         for (Gene currentGene : geneList) {
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java
index fdbd0fd35b..b7a259ff35 100644
--- a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java
+++ b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java
@@ -587,8 +587,8 @@ private List<VariantAnnotation> runAnnotationProcess(List<Variant> normalizedVar
 
             if (annotatorSet.contains("consequenceType")) {
                 try {
-                    List<ConsequenceType> consequenceTypeList = getConsequenceTypeList(variant, affectedGenes, true, QueryOptions.empty(),
-                            dataRelease);
+                    List<ConsequenceType> consequenceTypeList = getConsequenceTypeList(variant, affectedGenes, true,
+                            new QueryOptions().append("imprecise", imprecise).append("cnvExtraPadding", cnvExtraPadding), dataRelease);
                     variantAnnotation.setConsequenceTypes(consequenceTypeList);
                     if (phased) {
                         checkAndAdjustPhasedConsequenceTypes(variant, variantBuffer, dataRelease);
@@ -1308,6 +1308,9 @@ private boolean[] getRegulatoryRegionOverlaps(Variant variant) throws QueryExcep
             return getRegulatoryRegionOverlaps(variant.getChromosome(), variant.getStart());
         } else if (VariantType.INDEL.equals(variant.getType()) && StringUtils.isBlank(variant.getReference())) {
             return getRegulatoryRegionOverlaps(variant.getChromosome(), variant.getStart() - 1, variant.getEnd());
+        } else if (VariantType.CNV.equals(variant.getType())) {
+            return getRegulatoryRegionOverlaps(variant.getChromosome(), variant.getStart() - cnvExtraPadding,
+                    variant.getEnd() + cnvExtraPadding);
             // Short deletions and symbolic variants except breakends
         } else if (!VariantType.BREAKEND.equals(variant.getType())) {
             return getRegulatoryRegionOverlaps(variant.getChromosome(), variant.getStart(), variant.getEnd());
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantAnnotationCalculatorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantAnnotationCalculatorTest.java
index e1edc55cdc..c7e790bf81 100644
--- a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantAnnotationCalculatorTest.java
+++ b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantAnnotationCalculatorTest.java
@@ -33,6 +33,7 @@
 import org.opencb.cellbase.lib.GenericMongoDBAdaptorTest;
 import org.opencb.cellbase.lib.variant.annotation.VariantAnnotationCalculator;
 import org.opencb.commons.datastore.core.QueryOptions;
+import org.opencb.commons.datastore.core.result.QueryResult;
 
 import java.io.IOException;
 import java.nio.file.Path;
@@ -1957,6 +1958,39 @@ public void testGetAllConsequenceTypesByVariant() throws IOException, QueryExcep
 //        }
     }
 
+    @Test
+    // long variant should have same annotations as short variant + cnvPadding
+    public void testCNVExtraPadding() throws Exception {
+
+        // short variant
+        Variant shortVariant = new Variant("chr17:43087248-43087249:<CNV>");
+        // long variant
+        Variant longVariant = new Variant("chr17:43087248-43098506:<CNV>");
+
+        QueryOptions queryOptions = new QueryOptions("useCache", false);
+        queryOptions.put("include", "consequenceType, reference, alternate ,clinical");
+        queryOptions.put("normalize", true);
+        queryOptions.put("skipDecompose", false);
+        queryOptions.put("checkAminoAcidChange", true);
+        queryOptions.put("imprecise", true);
+        queryOptions.put("phased", false);
+
+        // long variant
+        CellBaseDataResult<ConsequenceType> consequenceTypeResult =
+                variantAnnotationCalculator.getAllConsequenceTypesByVariant(longVariant, queryOptions);
+        assertEquals(27, consequenceTypeResult.getNumResults());
+
+        // short variant
+        consequenceTypeResult = variantAnnotationCalculator.getAllConsequenceTypesByVariant(shortVariant, queryOptions);
+        assertEquals(27, consequenceTypeResult.getNumResults());
+
+        queryOptions.put("cnvExtraPadding", 10000);
+
+        // short variant with padding
+        consequenceTypeResult = variantAnnotationCalculator.getAllConsequenceTypesByVariant(shortVariant, queryOptions);
+        assertEquals(27, consequenceTypeResult.getNumResults());
+    }
+
     private <T> void assertObjectListEquals(String expectedConsequenceTypeJson, List<T> actualList,
                                             Class<T> clazz) throws IOException {
         ObjectReader reader = jsonObjectMapper