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fix: SvAnna scores now calculated for >1kb non-symbolic SV insertions #634

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fix: SvAnna scores now calculated for >1kb non-symbolic SV insertions #634

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2 changes: 1 addition & 1 deletion exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/VariantEvaluation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -409,7 +409,7 @@ public float pathogenicityScore() {

private float variantEffectScore() {
float variantEffectScore = VariantEffectPathogenicityScore.pathogenicityScoreOf(variantEffect);
if (this.isSymbolic()) {
if (this.isSymbolic() || Math.abs(this.changeLength()) >= 1000) {
// SvAnna scoring https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-022-01046-6/tables/1
// | element contains v
// class | v contains t | v overlaps t | Coding or splice | UTR | Intronic | Promoter
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17 changes: 17 additions & 0 deletions ...r-core/src/test/java/org/monarchinitiative/exomiser/core/model/VariantEvaluationTest.java
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Expand Up @@ -473,6 +473,23 @@ void testSymbolicInsertionScores(String alt, VariantEffect variantEffect, float
assertThat(sv.pathogenicityScore(), equalTo(expected));
}

@ParameterizedTest
@CsvSource({
"CODING_SEQUENCE_VARIANT, 0.2",
"SPLICE_REGION_VARIANT, 0.9",
"CODING_TRANSCRIPT_VARIANT, 0.0",
"SEQUENCE_VARIANT, 0.0",
})
void testLargeNonSymbolicInsertionScores(VariantEffect variantEffect, float expected) {
// Non-symbolic insertions >= 1000bp are routed to the structural variant annotator and should
// receive SvAnna-based scoring, not the default SEQUENCE_VARIANT score of 0.0
String longAlt = "A".repeat(1001);
VariantEvaluation sv = newBuilder(2, 1, 1, "A", longAlt, 1000)
.variantEffect(variantEffect)
.build();
assertThat(sv.pathogenicityScore(), equalTo(expected));
}

@Test
public void testFailedFilterTypesDontContainPassedFilterTypes() {
Set<FilterType> expectedFilters = EnumSet.of(FAIL_FREQUENCY_RESULT.filterType());
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