Copy number amplification
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Gain-of-Function
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Amplification
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Gene fusion
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Gain-of-Function
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Fusion
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Non-targeted fusion
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Gain-of-Function
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NonTargetedFusion
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- SVTYPE = "Fusion"
- FILTER = "PASS"
- Non-Targeted field is present
- NT_FUSION_IN_FRAME is not FALSE
- NT_FUSION_DRIVER_INVOLVED is not FALSE
- NT_FUSION_SECONDARY is not TRUE
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RNA exon variant
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Gain-of-Function
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RNAExonVariant
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Loss-of-function truncating de novo mutation
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Loss-of-Function
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Truncating
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Positive mutation call
Functional impact is frameshift block substitution, frameshift deletion, frameshift insertion, or nonsense
Occurs in a de-novo calling gene
Meets de-novo thresholds
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Missense hotspot mutation
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Gain-of-Function
Loss-of-Function
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Hotspot
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In-frame hotspot mutation
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Gain-of-Function
Loss-of-Function
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Hotspot
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Splice site hotspot mutation
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Gain-of-Function
Loss-of-Function
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Hotspot
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Intronic hotspot mutation
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Gain-of-Function
Loss-of-Function
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Hotspot
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Loss-of-function truncating hotspot mutation
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Loss-of-Function
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Truncating
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Positive mutation call
Function, transcript, and coding syntax occur in predefined truncating hotspot list
Occurs in a loss-of-function gene
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MNV hotspot mutation
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Gain-of-Function
Loss-of-Function
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Hotspot
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EGFR exon 19 deletion[1]
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Gain-of-Function
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EGFRExon19Deletion
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Positive Hotspot mutation call
Functional impact is nonframeshift deletion, nonframeshift block substitution
Deletion impacts codons 744–761 of EGFR
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EGFR exon 20 insertion1
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Gain-of-Function
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EGFRExon20Insertion
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Positive Hotspot mutation call
Functional impact is nonframeshift insertion, nonframeshift block substitution
Insertion impacts codons 762–775 of EGFR or variant is in EGFR exon 20 insertion confirmed list
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ERBB2 exon 20 insertion1
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Gain-of-Function
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ERBB2Exon20Insertion
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Positive Hotspot mutation call
Functional impact is nonframeshift insertion, nonframeshift block substitution
Insertion impacts codons 770–783 of ERBB2
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KIT exon 11 deletion1
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Gain-of-Function
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KITExon11Deletion
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Positive Hotspot mutation call
Functional impact is nonframeshift deletion, or nonframeshift block substitution
Deletion impacts codons 550-580 of KIT
Alternatively, mutation occurs in splice site flanking the 5' end of exon 11
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KIT exon 11 insertion1
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Gain-of-Function
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KITExon11Insertion
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Positive Hotspot mutation call
Functional impact is nonframeshift insertion, or nonframeshift block substitution
Insertion impacts codons 550-580 of KIT
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MET exon 14 skipping1
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Gain-of-Function
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METExon14Skipping
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Positive Hotspot mutation call
Location is splice site in MET exon 14, is intronic >= 4bp deletion in 30 nucleotides preceding MET exon 14, or variant is in MET Exon 14 Skipping confirmed list
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PDGFRA exon 18 deletion1
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Gain-of-Function
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PDGFRAExon18Deletion
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Positive Hotspot mutation call
Functional impact is nonframeshift deletion, or nonframeshift block substitution
Deletion impacts codons 841-847 of PDGFRA
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