Alter ClinVarData alleleId to variationId for direct links to the Cli…

…nVar website.
exomiser · Jan 18, 2024 · 9cfa3d4 · 9cfa3d4
1 parent e212a31
commit 9cfa3d4
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Showing 28 changed files with 84 additions and 101 deletions.
diff --git a/...core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/SvPathogenicityDao.java b/...core/src/main/java/org/monarchinitiative/exomiser/core/genome/dao/SvPathogenicityDao.java
@@ -194,7 +194,7 @@ private List<SvResult> processSvResults(ResultSet rs, Variant variant) throws SQ
             if (SvMetaType.isEquivalent(variant.variantType(), variantType)) {
                 ClinVarData.ClinSig sig = ClinVarData.ClinSig.valueOf(clinSig);
                 ClinVarData clinVarData = ClinVarData.builder()
-                        .alleleId(alleleId)
+                        .variationId(alleleId)
                         .primaryInterpretation(sig)
                         .reviewStatus(clinRevStat)
                         .build();

diff --git a/...iser-core/src/main/java/org/monarchinitiative/exomiser/core/model/AlleleProtoAdaptor.java b/...iser-core/src/main/java/org/monarchinitiative/exomiser/core/model/AlleleProtoAdaptor.java
@@ -160,7 +160,6 @@ public static ClinVarData toClinVarData(ClinVar clinVar) {
             return ClinVarData.empty();
         }
         ClinVarData.Builder builder = ClinVarData.builder();
-        builder.alleleId(clinVar.getAlleleId());
         builder.variationId(clinVar.getVariationId());
         builder.primaryInterpretation(toClinSig(clinVar.getPrimaryInterpretation()));
         builder.conflictingInterpretationCounts(toConflictCounts(clinVar.getClinSigCountsMap()));

diff --git a/...re/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/ClinVarData.java b/...re/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/ClinVarData.java
@@ -56,8 +56,7 @@ public enum ClinSig {
         RISK_FACTOR
     }
 
-    //https://www.ncbi.nlm.nih.gov/clinvar/?term=99222[alleleid]
-    private final String alleleId;
+    //https://www.ncbi.nlm.nih.gov/clinvar/variation/99222
     private final String variationId;
     private final ClinSig primaryInterpretation;
     private final Map<ClinSig, Integer> conflictingInterpretationCounts;
@@ -117,7 +116,6 @@ public enum ClinSig {
     //##INFO=<ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes. One or more of the following values may be added: 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
 
     private ClinVarData(Builder builder) {
-        this.alleleId = builder.alleleId;
         this.variationId = builder.variationId;
         this.primaryInterpretation = builder.primaryInterpretation;
         Map<ClinSig, Integer> map = new EnumMap<>(ClinSig.class);
@@ -141,10 +139,6 @@ public boolean isEmpty() {
         return this.equals(EMPTY);
     }
 
-    public String getAlleleId() {
-        return alleleId;
-    }
-
     public String getVariationId() {
         return variationId;
     }
@@ -232,7 +226,7 @@ public boolean equals(Object o) {
         if (this == o) return true;
         if (o == null || getClass() != o.getClass()) return false;
         ClinVarData that = (ClinVarData) o;
-        return Objects.equals(alleleId, that.alleleId) &&
+        return Objects.equals(variationId, that.variationId) &&
                primaryInterpretation == that.primaryInterpretation &&
                Objects.equals(secondaryInterpretations, that.secondaryInterpretations) &&
                Objects.equals(reviewStatus, that.reviewStatus) &&
@@ -241,14 +235,13 @@ public boolean equals(Object o) {
 
     @Override
     public int hashCode() {
-        return Objects.hash(alleleId, primaryInterpretation, secondaryInterpretations, reviewStatus, includedAlleles);
+        return Objects.hash(variationId, primaryInterpretation, secondaryInterpretations, reviewStatus, includedAlleles);
     }
 
     @Override
     public String toString() {
         return "ClinVarData{" +
                "variationId='" + variationId + '\'' +
-               ", alleleId='" + alleleId + '\'' +
                ", geneSymbol='" + geneSymbol + '\'' +
                ", hgvsCdna='" + hgvsCdna + '\'' +
                ", hgvsProtein='" + hgvsProtein + '\'' +
@@ -264,7 +257,6 @@ public String toString() {
     public Builder toBuilder() {
         return new Builder()
                 .variationId(variationId)
-                .alleleId(alleleId)
                 .primaryInterpretation(primaryInterpretation)
                 .secondaryInterpretations(secondaryInterpretations)
                 .reviewStatus(reviewStatus)
@@ -282,7 +274,6 @@ public static Builder builder() {
     }
 
     public static class Builder {
-        private String alleleId = "";
         private String variationId = "";
         private ClinSig primaryInterpretation = ClinSig.NOT_PROVIDED;
         private Set<ClinSig> secondaryInterpretations = EnumSet.noneOf(ClinSig.class);

diff --git a/.../main/java/org/monarchinitiative/exomiser/core/writers/TsvVariantAllMoiResultsWriter.java b/.../main/java/org/monarchinitiative/exomiser/core/writers/TsvVariantAllMoiResultsWriter.java
@@ -71,7 +71,7 @@ public class TsvVariantAllMoiResultsWriter implements ResultsWriter {
             .withQuote(null)
             .withRecordSeparator("\n")
             .withIgnoreSurroundingSpaces(true)
-            .withHeader("#RANK", "ID", "GENE_SYMBOL", "ENTREZ_GENE_ID", "MOI", "P-VALUE", "EXOMISER_GENE_COMBINED_SCORE", "EXOMISER_GENE_PHENO_SCORE", "EXOMISER_GENE_VARIANT_SCORE", "EXOMISER_VARIANT_SCORE", "CONTRIBUTING_VARIANT", "WHITELIST_VARIANT", "VCF_ID", "RS_ID", "CONTIG", "START", "END", "REF", "ALT", "CHANGE_LENGTH", "QUAL", "FILTER", "GENOTYPE", "FUNCTIONAL_CLASS", "HGVS", "EXOMISER_ACMG_CLASSIFICATION", "EXOMISER_ACMG_EVIDENCE", "EXOMISER_ACMG_DISEASE_ID", "EXOMISER_ACMG_DISEASE_NAME", "CLINVAR_ALLELE_ID", "CLINVAR_PRIMARY_INTERPRETATION", "CLINVAR_STAR_RATING", "GENE_CONSTRAINT_LOEUF", "GENE_CONSTRAINT_LOEUF_LOWER", "GENE_CONSTRAINT_LOEUF_UPPER", "MAX_FREQ_SOURCE", "MAX_FREQ", "ALL_FREQ", "MAX_PATH_SOURCE", "MAX_PATH", "ALL_PATH");
+            .withHeader("#RANK", "ID", "GENE_SYMBOL", "ENTREZ_GENE_ID", "MOI", "P-VALUE", "EXOMISER_GENE_COMBINED_SCORE", "EXOMISER_GENE_PHENO_SCORE", "EXOMISER_GENE_VARIANT_SCORE", "EXOMISER_VARIANT_SCORE", "CONTRIBUTING_VARIANT", "WHITELIST_VARIANT", "VCF_ID", "RS_ID", "CONTIG", "START", "END", "REF", "ALT", "CHANGE_LENGTH", "QUAL", "FILTER", "GENOTYPE", "FUNCTIONAL_CLASS", "HGVS", "EXOMISER_ACMG_CLASSIFICATION", "EXOMISER_ACMG_EVIDENCE", "EXOMISER_ACMG_DISEASE_ID", "EXOMISER_ACMG_DISEASE_NAME", "CLINVAR_VARIATION_ID", "CLINVAR_PRIMARY_INTERPRETATION", "CLINVAR_STAR_RATING", "GENE_CONSTRAINT_LOEUF", "GENE_CONSTRAINT_LOEUF_LOWER", "GENE_CONSTRAINT_LOEUF_UPPER", "MAX_FREQ_SOURCE", "MAX_FREQ", "ALL_FREQ", "MAX_PATH_SOURCE", "MAX_PATH", "ALL_PATH");
     private final DecimalFormat decimalFormat = new DecimalFormat("0.0000");
 
     public TsvVariantAllMoiResultsWriter() {
@@ -162,7 +162,7 @@ private List<Object> buildVariantRecord(int rank, VariantEvaluation ve, GeneScor
         fields.add(assignment.map(acmgAssignment -> acmgAssignment.disease().getDiseaseName()).orElse(""));
         PathogenicityData pathogenicityData = ve.getPathogenicityData();
         ClinVarData clinVarData = pathogenicityData.getClinVarData();
-        fields.add(clinVarData.getAlleleId());
+        fields.add(clinVarData.getVariationId());
         fields.add(clinVarData.getPrimaryInterpretation());
         fields.add(clinVarData.starRating());
         GeneConstraint geneConstraint = GeneConstraints.geneContraint(geneIdentifier.getGeneSymbol());

diff --git a/...re/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvVariantResultsWriter.java b/...re/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvVariantResultsWriter.java
@@ -71,7 +71,7 @@ public class TsvVariantResultsWriter implements ResultsWriter {
             .withSkipHeaderRecord()
             .withRecordSeparator("\n")
             .withIgnoreSurroundingSpaces(true)
-            .withHeader("#RANK", "ID", "GENE_SYMBOL", "ENTREZ_GENE_ID", "MOI", "P-VALUE", "EXOMISER_GENE_COMBINED_SCORE", "EXOMISER_GENE_PHENO_SCORE", "EXOMISER_GENE_VARIANT_SCORE", "EXOMISER_VARIANT_SCORE", "CONTRIBUTING_VARIANT", "WHITELIST_VARIANT", "VCF_ID", "RS_ID", "CONTIG", "START", "END", "REF", "ALT", "CHANGE_LENGTH", "QUAL", "FILTER", "GENOTYPE", "FUNCTIONAL_CLASS", "HGVS", "EXOMISER_ACMG_CLASSIFICATION", "EXOMISER_ACMG_EVIDENCE", "EXOMISER_ACMG_DISEASE_ID", "EXOMISER_ACMG_DISEASE_NAME", "CLINVAR_ALLELE_ID", "CLINVAR_PRIMARY_INTERPRETATION", "CLINVAR_STAR_RATING", "GENE_CONSTRAINT_LOEUF", "GENE_CONSTRAINT_LOEUF_LOWER", "GENE_CONSTRAINT_LOEUF_UPPER", "MAX_FREQ_SOURCE", "MAX_FREQ", "ALL_FREQ", "MAX_PATH_SOURCE", "MAX_PATH", "ALL_PATH");
+            .withHeader("#RANK", "ID", "GENE_SYMBOL", "ENTREZ_GENE_ID", "MOI", "P-VALUE", "EXOMISER_GENE_COMBINED_SCORE", "EXOMISER_GENE_PHENO_SCORE", "EXOMISER_GENE_VARIANT_SCORE", "EXOMISER_VARIANT_SCORE", "CONTRIBUTING_VARIANT", "WHITELIST_VARIANT", "VCF_ID", "RS_ID", "CONTIG", "START", "END", "REF", "ALT", "CHANGE_LENGTH", "QUAL", "FILTER", "GENOTYPE", "FUNCTIONAL_CLASS", "HGVS", "EXOMISER_ACMG_CLASSIFICATION", "EXOMISER_ACMG_EVIDENCE", "EXOMISER_ACMG_DISEASE_ID", "EXOMISER_ACMG_DISEASE_NAME", "CLINVAR_VARIATION_ID", "CLINVAR_PRIMARY_INTERPRETATION", "CLINVAR_STAR_RATING", "GENE_CONSTRAINT_LOEUF", "GENE_CONSTRAINT_LOEUF_LOWER", "GENE_CONSTRAINT_LOEUF_UPPER", "MAX_FREQ_SOURCE", "MAX_FREQ", "ALL_FREQ", "MAX_PATH_SOURCE", "MAX_PATH", "ALL_PATH");
 
     private final DecimalFormat decimalFormat = new DecimalFormat("0.0000");
 
@@ -164,7 +164,7 @@ private List<Object> buildVariantRecord(int rank, VariantEvaluation ve, GeneScor
         fields.add(assignment.map(acmgAssignment -> acmgAssignment.disease().getDiseaseName()).orElse(""));
         PathogenicityData pathogenicityData = ve.getPathogenicityData();
         ClinVarData clinVarData = pathogenicityData.getClinVarData();
-        fields.add(clinVarData.getAlleleId());
+        fields.add(clinVarData.getVariationId());
         fields.add(clinVarData.getPrimaryInterpretation());
         fields.add(clinVarData.starRating());
         GeneConstraint geneConstraint = GeneConstraints.geneContraint(geneIdentifier.getGeneSymbol());

diff --git a/exomiser-core/src/main/proto/allele.proto b/exomiser-core/src/main/proto/allele.proto
@@ -42,7 +42,7 @@ message ClinVar {
         RISK_FACTOR = 14;
     }
 
-    string alleleId = 1;
+    string alleleId = 1 [deprecated = true];
     ClinSig primaryInterpretation = 2;
     repeated ClinSig secondaryInterpretations = 3;
     string reviewStatus = 4;

diff --git a/exomiser-core/src/main/resources/templates/results.html b/exomiser-core/src/main/resources/templates/results.html
@@ -335,7 +335,7 @@ <h4>Variant Score: <b
                                       th:text="${clinVarData.getPrimaryInterpretation()}">PATHOGENIC</span>
                                 <span th:case="*" class="label label-default"
                                       th:text="${clinVarData.getPrimaryInterpretation()}">UNCERTAIN_SIGNIFICANCE</span>
-                                <a th:href="@{https://www.ncbi.nlm.nih.gov/clinvar/(term=${clinVarData.alleleId} + '[alleleid]')}"
+                                <a th:href="@{|https://www.ncbi.nlm.nih.gov/clinvar/variation/${clinVarData.variationId}|}"
                                    th:text="'(' + ${clinVarData.getReviewStatus()} + ')'">
                                     (criteria_provided,_single_submitter)
                                 </a>
@@ -479,7 +479,7 @@ <h4>Variant Score: <b
                                   th:text="${clinVarData.getPrimaryInterpretation()}">PATHOGENIC</span>
                             <span th:case="*" class="label label-default"
                                   th:text="${clinVarData.getPrimaryInterpretation()}">UNCERTAIN_SIGNIFICANCE</span>
-                            <a th:href="@{https://www.ncbi.nlm.nih.gov/clinvar/(term=${clinVarData.alleleId} + '[alleleid]')}"
+                            <a th:href="@{|https://www.ncbi.nlm.nih.gov/clinvar/variation/${clinVarData.variationId}|}"
                                th:text="'(' + ${clinVarData.getReviewStatus()} + ')'">
                                 (criteria_provided,_single_submitter)
                             </a>

diff --git a/.../src/test/java/org/monarchinitiative/exomiser/core/genome/VariantDataServiceImplTest.java b/.../src/test/java/org/monarchinitiative/exomiser/core/genome/VariantDataServiceImplTest.java
@@ -73,7 +73,7 @@ public class VariantDataServiceImplTest {
     @Mock
     private PathogenicityDao svPathogenicityDao;
 
-    private static final ClinVarData PATH_CLINVAR_DATA = ClinVarData.builder().alleleId("12345")
+    private static final ClinVarData PATH_CLINVAR_DATA = ClinVarData.builder().variationId("12345")
             .primaryInterpretation(ClinVarData.ClinSig.PATHOGENIC)
             .build();
     private static final PathogenicityData PATH_DATA = PathogenicityData.of(

diff --git a/...test/java/org/monarchinitiative/exomiser/core/genome/dao/PathogenicityDaoMvStoreTest.java b/...test/java/org/monarchinitiative/exomiser/core/genome/dao/PathogenicityDaoMvStoreTest.java
@@ -150,14 +150,14 @@ public void getPathogenicityDataJustClinVar() {
                 .build();
 
         AlleleKey key = AlleleProtoAdaptor.toAlleleKey(variant);
-        ClinVar clinVar = ClinVar.newBuilder().setAlleleId("54321").setPrimaryInterpretation(ClinVar.ClinSig.ASSOCIATION).build();
+        ClinVar clinVar = ClinVar.newBuilder().setVariationId("54321").setPrimaryInterpretation(ClinVar.ClinSig.ASSOCIATION).build();
         AlleleProperties properties = AlleleProperties.newBuilder()
                 .setClinVar(clinVar)
                 .build();
 
         PathogenicityDao instance = newInstanceWithData(ImmutableMap.of(key, properties));
         PathogenicityData expected = PathogenicityData.of(ClinVarData.builder()
-                .alleleId("54321")
+                .variationId("54321")
                 .primaryInterpretation(ClinVarData.ClinSig.ASSOCIATION)
                 .build());
         assertThat(instance.getPathogenicityData(variant), equalTo(expected));
@@ -171,7 +171,7 @@ public void getPathogenicityDataAll() throws Exception {
 
         AlleleKey key = AlleleProtoAdaptor.toAlleleKey(variant);
         ClinVar clinVar = ClinVar.newBuilder()
-                .setAlleleId("54321")
+                .setVariationId("54321")
                 .setPrimaryInterpretation(ClinVar.ClinSig.PATHOGENIC)
                 .build();
         AlleleProperties properties = AlleleProperties.newBuilder()
@@ -184,7 +184,7 @@ public void getPathogenicityDataAll() throws Exception {
         PathogenicityDao instance = newInstanceWithData(ImmutableMap.of(key, properties));
 
         PathogenicityData expected = PathogenicityData.of(ClinVarData.builder()
-                .alleleId("54321")
+                .variationId("54321")
                 .primaryInterpretation(ClinVarData.ClinSig.PATHOGENIC)
                 .build(),
                 SiftScore.of(0f), PolyPhenScore.of(1f), MutationTasterScore.of(1f));

diff --git a/...-core/src/test/java/org/monarchinitiative/exomiser/core/model/AlleleProtoAdaptorTest.java b/...-core/src/test/java/org/monarchinitiative/exomiser/core/model/AlleleProtoAdaptorTest.java
@@ -21,6 +21,7 @@
 package org.monarchinitiative.exomiser.core.model;
 
 import com.google.common.collect.ImmutableMap;
+import de.charite.compbio.jannovar.annotation.VariantEffect;
 import org.junit.jupiter.api.Test;
 import org.monarchinitiative.exomiser.core.genome.TestFactory;
 import org.monarchinitiative.exomiser.core.model.frequency.Frequency;
@@ -145,7 +146,7 @@ public void parseClinVarDataDefaultInstanceReturnsEmpty() {
     public void parseClinVarData() {
 
         ClinVar clinVar = ClinVar.newBuilder()
-                .setAlleleId("12345")
+                .setVariationId("12345")
                 .setPrimaryInterpretation(ClinVar.ClinSig.CONFLICTING_PATHOGENICITY_INTERPRETATIONS)
                 .addSecondaryInterpretations(ClinVar.ClinSig.PATHOGENIC_OR_LIKELY_PATHOGENIC)
                 .addSecondaryInterpretations(ClinVar.ClinSig.UNCERTAIN_SIGNIFICANCE)
@@ -157,7 +158,7 @@ public void parseClinVarData() {
                 .build();
 
         ClinVarData expected = ClinVarData.builder()
-                .alleleId("12345")
+                .variationId("12345")
                 .primaryInterpretation(ClinVarData.ClinSig.CONFLICTING_PATHOGENICITY_INTERPRETATIONS)
                 .secondaryInterpretations(EnumSet.of(
                         ClinVarData.ClinSig.PATHOGENIC_OR_LIKELY_PATHOGENIC,

diff --git a/...rc/test/java/org/monarchinitiative/exomiser/core/model/pathogenicity/ClinVarDataTest.java b/...rc/test/java/org/monarchinitiative/exomiser/core/model/pathogenicity/ClinVarDataTest.java
@@ -39,7 +39,7 @@ public class ClinVarDataTest {
     public void testEmptyBuilder() {
         ClinVarData instance = ClinVarData.builder().build();
 
-        assertThat(instance.getAlleleId(), equalTo(""));
+        assertThat(instance.getVariationId(), equalTo(""));
         assertThat(instance.getPrimaryInterpretation(), equalTo(ClinSig.NOT_PROVIDED));
         assertThat(instance.getSecondaryInterpretations(), equalTo(Collections.emptySet()));
         assertThat(instance.getReviewStatus(), equalTo(""));
@@ -58,7 +58,6 @@ public void testBuilderWithValues() {
         Map<String, ClinSig> included = Map.of("54321", ClinSig.PATHOGENIC_OR_LIKELY_PATHOGENIC);
         ClinVarData instance = ClinVarData.builder()
                 .variationId(variationId)
-                .alleleId(alleleId)
                 .geneSymbol(geneSymbol)
                 .variantEffect(variantEffect)
                 .primaryInterpretation(clinSig)
@@ -67,7 +66,6 @@ public void testBuilderWithValues() {
                 .includedAlleles(included)
                 .build();
 
-        assertThat(instance.getAlleleId(), equalTo(alleleId));
         assertThat(instance.getVariationId(), equalTo(variationId));
         assertThat(instance.getGeneSymbol(), equalTo(geneSymbol));
         assertThat(instance.getVariantEffect(), equalTo(variantEffect));
@@ -86,7 +84,6 @@ public void testStringValue() {
         String reviewStatus = "multiple_submitters,_no_conflict";
         Map<String, ClinSig> included = Map.of("54321", ClinSig.PATHOGENIC_OR_LIKELY_PATHOGENIC);
         ClinVarData instance = ClinVarData.builder()
-                .alleleId(alleleId)
                 .primaryInterpretation(clinSig)
                 .secondaryInterpretations(secondaryInterpretations)
                 .reviewStatus(reviewStatus)

diff --git a/...t/java/org/monarchinitiative/exomiser/core/model/pathogenicity/PathogenicityDataTest.java b/...t/java/org/monarchinitiative/exomiser/core/model/pathogenicity/PathogenicityDataTest.java
@@ -233,7 +233,7 @@ public void testEmptyClinVarData() {
 
     @Test
     public void testClinVarData() {
-        ClinVarData clinVarData = ClinVarData.builder().alleleId("12345").primaryInterpretation(ClinVarData.ClinSig.PATHOGENIC).build();
+        ClinVarData clinVarData = ClinVarData.builder().variationId("12345").primaryInterpretation(ClinVarData.ClinSig.PATHOGENIC).build();
         PathogenicityData instance = PathogenicityData.of(clinVarData, POLYPHEN_PASS);
         assertThat(instance.hasClinVarData(), is(true));
         assertThat(instance.getClinVarData(), equalTo(clinVarData));

diff --git a/...rc/test/java/org/monarchinitiative/exomiser/core/writers/TsvVariantResultsWriterTest.java b/...rc/test/java/org/monarchinitiative/exomiser/core/writers/TsvVariantResultsWriterTest.java
@@ -61,7 +61,7 @@ public class TsvVariantResultsWriterTest {
 
     private final TsvVariantResultsWriter instance = new TsvVariantResultsWriter();
 
-    private static final String HEADER = "#RANK\tID\tGENE_SYMBOL\tENTREZ_GENE_ID\tMOI\tP-VALUE\tEXOMISER_GENE_COMBINED_SCORE\tEXOMISER_GENE_PHENO_SCORE\tEXOMISER_GENE_VARIANT_SCORE\tEXOMISER_VARIANT_SCORE\tCONTRIBUTING_VARIANT\tWHITELIST_VARIANT\tVCF_ID\tRS_ID\tCONTIG\tSTART\tEND\tREF\tALT\tCHANGE_LENGTH\tQUAL\tFILTER\tGENOTYPE\tFUNCTIONAL_CLASS\tHGVS\tEXOMISER_ACMG_CLASSIFICATION\tEXOMISER_ACMG_EVIDENCE\tEXOMISER_ACMG_DISEASE_ID\tEXOMISER_ACMG_DISEASE_NAME\tCLINVAR_ALLELE_ID\tCLINVAR_PRIMARY_INTERPRETATION\tCLINVAR_STAR_RATING\tGENE_CONSTRAINT_LOEUF\tGENE_CONSTRAINT_LOEUF_LOWER\tGENE_CONSTRAINT_LOEUF_UPPER\tMAX_FREQ_SOURCE\tMAX_FREQ\tALL_FREQ\tMAX_PATH_SOURCE\tMAX_PATH\tALL_PATH\n";
+    private static final String HEADER = "#RANK\tID\tGENE_SYMBOL\tENTREZ_GENE_ID\tMOI\tP-VALUE\tEXOMISER_GENE_COMBINED_SCORE\tEXOMISER_GENE_PHENO_SCORE\tEXOMISER_GENE_VARIANT_SCORE\tEXOMISER_VARIANT_SCORE\tCONTRIBUTING_VARIANT\tWHITELIST_VARIANT\tVCF_ID\tRS_ID\tCONTIG\tSTART\tEND\tREF\tALT\tCHANGE_LENGTH\tQUAL\tFILTER\tGENOTYPE\tFUNCTIONAL_CLASS\tHGVS\tEXOMISER_ACMG_CLASSIFICATION\tEXOMISER_ACMG_EVIDENCE\tEXOMISER_ACMG_DISEASE_ID\tEXOMISER_ACMG_DISEASE_NAME\tCLINVAR_VARIATION_ID\tCLINVAR_PRIMARY_INTERPRETATION\tCLINVAR_STAR_RATING\tGENE_CONSTRAINT_LOEUF\tGENE_CONSTRAINT_LOEUF_LOWER\tGENE_CONSTRAINT_LOEUF_UPPER\tMAX_FREQ_SOURCE\tMAX_FREQ\tALL_FREQ\tMAX_PATH_SOURCE\tMAX_PATH\tALL_PATH\n";
 
     private AnalysisResults buildAnalysisResults() {
 

diff --git a/...me/src/main/java/org/monarchinitiative/exomiser/data/genome/indexers/AlleleConverter.java b/...me/src/main/java/org/monarchinitiative/exomiser/data/genome/indexers/AlleleConverter.java
@@ -83,7 +83,6 @@ private static void addClinVarData(AlleleProperties.Builder builder, Allele alle
 
     public static ClinVar toProtoClinVar(ClinVarData clinVarData) {
         ClinVar.Builder builder = ClinVar.newBuilder();
-        builder.setAlleleId(clinVarData.getAlleleId());
         builder.setVariationId(clinVarData.getVariationId());
         builder.setPrimaryInterpretation(toProtoClinSig(clinVarData.getPrimaryInterpretation()));
         for (Map.Entry<ClinVarData.ClinSig, Integer> entry : clinVarData.getConflictingInterpretationCounts().entrySet()) {
@@ -98,6 +97,8 @@ public static ClinVar toProtoClinVar(ClinVarData clinVarData) {
         }
         builder.setGeneSymbol(clinVarData.getGeneSymbol());
         builder.setVariantEffect(toProtoVariantEffect(clinVarData.getVariantEffect()));
+        builder.setHgvsCdna(clinVarData.getHgvsCdna());
+        builder.setHgvsProtein(clinVarData.getHgvsProtein());
         return builder.build();
     }
 

diff --git a/...rg/monarchinitiative/exomiser/data/genome/indexers/ClinVarWhiteListFileAlleleIndexer.java b/...rg/monarchinitiative/exomiser/data/genome/indexers/ClinVarWhiteListFileAlleleIndexer.java
@@ -107,7 +107,7 @@ private boolean isPathOrLikelyPath(ClinVarData clinVarData) {
 
     private StringJoiner createClinVarInfo(ClinVarData clinVarData) {
         StringJoiner stringJoiner = new StringJoiner(";");
-        stringJoiner.add("ALLELEID=" + clinVarData.getAlleleId());
+        stringJoiner.add("VARIATIONID=" + clinVarData.getVariationId());
         stringJoiner.add("CLNSIG=" + clinVarData.getPrimaryInterpretation());
         stringJoiner.add("CLNREVSTAT=" + clinVarData.getReviewStatus().replace(" ", "_"));
         stringJoiner.add("STARS=" + clinVarData.starRating());