Starting
Initialising…
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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 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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