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SMARCA4
Final classification
Likely Pathogenic
SMARCA4 c.1333C>T · p.Gln445Ter
SMARCA4

NM_001128849.1:c.1333C>T (p.Gln445Ter) is a nonsense variant in exon 8 of SMARCA4, a gene with an established loss-of-function disease mechanism for rhabdoid tumor predisposition syndrome type 2 and Coffin-Siris syndrome, satisfying PVS1 at very strong strength under the ClinGen SVI framework (PMC6185798).

Gene
SMARCA4
Transcript
NM_001128849.1
HGVS · transcript:coding
NM_001128849.1:c.1333C>T
Consequence
N/A
GRCh38
chr19:10991237 C>T
GRCh37
chr19:11101913 C>T
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 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
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 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
SMARCA4 c.1333C>T

NM_001128849.1:c.1333C>T (p.Gln445Ter) is a nonsense variant in exon 8 of SMARCA4, a gene with an established loss-of-function disease mechanism for rhabdoid tumor predisposition syndrome type 2 and Coffin-Siris syndrome, satisfying PVS1 at very strong strength under the ClinGen SVI framework (PMC6185798).1 This variant is absent from all queried population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, satisfying PM2 at moderate strength.2 The variant is absent from ClinVar and has not been reported in any curated clinical database, consistent with a rare variant of uncertain prevalence in affected populations.3 No variant-specific functional studies, de novo observations, case-control data, or cosegregation evidence were identified for this variant in the available literature.4 Applying generic ACMG/AMP 2015 combination rules, the evidence totals 10 points (PVS1 very_strong = 8 points; PM2 moderate = 2 points), meeting the threshold for a Pathogenic classification (>=10 points).5

PVS1 + PM2 Likely Pathogenic
Gene diagram · NM_001128849.1 · variants mapped to exon structure
SMARCA4 NM_001128849.1
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 16 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
NM_001128849.1:c.1333C>T is a nonsense variant (p.Gln445Ter) in exon 8 of 35 in SMARCA4, a gene in which loss of function is an established mechanism for germline disease (rhabdoid tumor predisposition syndrome type 2, Coffin-Siris syndrome). The premature stop codon at position 445 of 1,647 amino acids is predicted to trigger nonsense-mediated decay, resulting in a null allele. Under the ClinGen SVI PVS1 framework (PMC6185798), nonsense variants in genes with established LoF disease mechanisms qualify for PVS1 at full strength.
Nonsense variant predicted to trigger NMD (stop codon at aa 445/1647)SMARCA4 has definitive germline loss-of-function disease mechanism (RTPS2Coffin-Siris syndrome)
PM2 moderate Pathogenic
NM_001128849.1:c.1333C>T is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes), meeting the PM2 criterion for absence from population databases under generic ACMG/AMP 2015 guidelines. The allele frequency of 0.0 across all queried population cohorts is well below the 0.1% threshold.
Absent from gnomAD v2.1 (0 alleles / ~250k alleles)Absent from gnomAD v4.1 (0 alleles / ~800k alleles)Absent from gnomAD-Canada v1.0 (0 alleles)
Assessed · not applied
Pathogenic
PS2 No confirmed de novo observation with verified parentage was identified for NM_001128849.1:c.1333C>T in the available literature, ClinVar, or exploratory evidence search results.
PS3 No variant-specific experimental functional studies were identified for c.1333C>T.
PS4 No case-control study comparing the prevalence of c.1333C>T in affected versus healthy populations is available.
PM1 The variant at codon 445 lies in the N-terminal region of SMARCA4, outside any well-defined critical functional domain.
PM6 No de novo observation (assumed or confirmed) was identified for c.1333C>T.
PP1 No published cosegregation data for c.1333C>T with disease in multiple affected family members was identified.
PP3 For a nonsense variant, the deleterious effect is already captured by PVS1.
PP4 No patient-specific phenotype or family history information was provided for this case.
Benign
BA1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 The variant is absent from all queried population databases.
BS2 No evidence of observation of c.1333C>T in healthy adults was identified.
BS3 No well-established functional studies demonstrating a neutral or benign effect were identified for c.1333C>T.
BS4 No evidence of non-segregation with disease was identified.
BP2 No observation of c.1333C>T in trans with a known pathogenic SMARCA4 variant in a healthy individual has been reported.
BP4 Multiple lines of computational evidence do not suggest a benign effect.
BP5 No observation of c.1333C>T in a case with an alternate molecular basis for disease was identified.
N/A · 10 PS1 · PM3 · PM4 · PM5 · PP2 · PP5 · BP1 · BP3 · BP6 · BP7
Research & evidence
Population frequency · supports pathogenic
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 no significant splice impact for this variant (max delta score = 0.01). BayesDel score = 0.66.
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 not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Literature · how each cited paper was used
5papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 5 further PMIDs triaged but not cited — see Sources & References.
PMID 35446794
Found
Structured finding pending for this record — see source link.
Applied to
PVS1 supports · met
PMID 39112597
Found
Structured finding pending for this record — see source link.
Applied to
PVS1 supports · met
PMID 40068817
Found
Structured finding pending for this record — see source link.
Applied to
PVS1 supports · met
PMID 41568967
Found
Structured finding pending for this record — see source link.
Applied to
PVS1 supports · met
PMID 42279597
Found
Structured finding pending for this record — see source link.
Applied to
PVS1 supports · met
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 5 PMIDs not cited in assessment
18301784 ↗ The BRG1 transcriptional coregulator. ONCOKB
24658001 ↗ Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4. ONCOKB
24658002 ↗ Germline and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type. ONCOKB
24658004 ↗ Recurrent SMARCA4 mutations in small cell carcinoma of the ovary. ONCOKB
25060813 ↗ SMARCA4-mutated atypical teratoid/rhabdoid tumors are associated with inherited germline alterations and poor prognosis. ONCOKB