Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
SETD2
Final classification
VUS
SETD2 c.7572dup · p.Lys2525Ter
SETD2

NM_014159.6:c.7572dup (p.Lys2525Ter) in SETD2 is a null variant in a gene for which loss of function is an established germline disease mechanism (SETD2 overgrowth syndrome), applied at PVS1_Moderate after downgrade for location in the last exon with predicted NMD escape and truncation of a non-critical C-terminal region.

Gene
SETD2
Transcript
NM_014159.6
HGVS · transcript:coding
NM_014159.6:c.7572dup
Consequence
N/A
GRCh38
chr3:47017215 T>TA
GRCh37
chr3:47058705 T>TA
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
Classification rationale
PVS1PM2 VUS
SETD2 c.7572dup

NM_014159.6:c.7572dup (p.Lys2525Ter) in SETD2 is a null variant in a gene for which loss of function is an established germline disease mechanism (SETD2 overgrowth syndrome), applied at PVS1_Moderate after downgrade for location in the last exon with predicted NMD escape and truncation of a non-critical C-terminal region.1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, and absent from ClinVar, satisfying PM2_Moderate for a rare variant at extremely low population frequency.2 No additional pathogenic, benign, or functional criteria are met. The three somatic-cancer publications reviewed (PMID:23417712, PMID:24509477, PMID:25728682) discuss SETD2 at the gene level but do not mention or characterize this specific variant. Overall classification: VUS (Variant of Uncertain Significance). Two moderate pathogenic criteria (PVS1_Moderate, PM2_Moderate) fall short of the Likely Pathogenic threshold under the ACMG/AMP 2015 combination rules, which require three moderate criteria or one strong plus one moderate for Likely Pathogenic. No benign criteria are met. The evidence is insufficient to classify this variant as either likely pathogenic or likely benign.3

PVS1 + PM2 VUS
1 pvs1_generic_framework ↗pvs1_gene_contextpvs1_variant_assessment
3 generic_acmg_combination_rules
Gene diagram · NM_014159.6 · variants mapped to exon structure
SETD2 NM_014159.6
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 moderate Pathogenic
This duplication (NM_014159.6:c.7572dup) creates a premature termination codon at p.Lys2525Ter in SETD2, a gene for which loss of function is an established germline disease mechanism (SETD2 overgrowth syndrome; PMID:24852293). However, the variant resides in exon 21 of 21 (the last exon) and is predicted to escape nonsense-mediated decay, producing a truncated protein lacking only the C-terminal ~40 amino acids of 2,565 total residues. The removed region is not a well-characterized functional domain. Per PMC6185798, this warrants downgrade from full PVS1 to PVS1_Moderate.
SETD2 germline loss-of-function mechanism established (PMID:24852293PMID:31643139)Variant creates premature stop codon p.Lys2525Ter in last exon (21/21)
PM2 moderate Pathogenic
This variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, and absent from ClinVar, satisfying PM2 for a rare variant at extremely low population frequency.
Absent from gnomAD v2.1 (exomes)Absent from gnomAD v4.1 (exomes)Absent from gnomAD-Canada v1.0 (genomes)
Assessed · not applied
Pathogenic
PS1 No pathogenic variant at the same amino acid residue (p.Lys2525) has been reported in ClinVar for comparison.
PS2 No de novo observation has been reported for this variant; absence of parental data precludes PS2 application.
PS3 No variant-specific functional data exists for NM_014159.6:c.7572dup.
PS4 This variant is absent from ClinVar and gnomAD population databases.
PM1 The variant truncates the C-terminal ~40 amino acids of SETD2.
PM5 No pathogenic missense variant at the same residue (p.Lys2525) was identified in ClinVar as a comparator.
PM6 No de novo observation has been reported for this variant; assumed de novo not applicable without at least one report.
PP1 No segregation data are available for this variant.
PP3 This is a truncating variant whose primary effect is premature protein termination, already accounted for under PVS1.
PP4 No patient phenotype or family history is available for assessment against the disease-specific presentation of SETD2 overgrowth syndrome.
PP5 This variant is absent from ClinVar.
Benign
BA1 The variant is absent from all population databases, with an allele frequency far below the BA1 threshold of >1%.
BS1 The variant is absent from population databases; allele frequency does not exceed the BS1 threshold of >0.3%.
BS2 The variant has not been observed in any healthy adult individual; absent from gnomAD.
BS3 No well-established in vitro or in vivo functional studies demonstrate a benign effect for this variant.
BS4 No family segregation data are available to demonstrate lack of cosegregation with disease.
BP2 No co-occurrence data are available; the variant has not been observed in trans with a pathogenic SETD2 variant or in any individual.
BP4 This variant creates a premature termination codon, which is predicted to alter the protein product.
BP5 No data on an alternate molecular basis for disease in a case harboring this variant are available.
BP6 This variant is absent from ClinVar.
N/A · 6 PM3 · PM4 · PP2 · BP1 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.38).
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV57443657, n = 3 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 3 PMIDs not cited in assessment
23417712 ↗ Mutations in SETD2 and genes affecting histone H3K36 methylation target hemispheric high-grade gliomas. ONCOKB
24509477 ↗ Identification of functional cooperative mutations of SETD2 in human acute leukemia. ONCOKB
25728682 ↗ SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair. ONCOKB