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SMARCA4
Final classification
Likely Pathogenic
SMARCA4 c.1944-1G>T · p.?
SMARCA4

NM_001128849.1:c.1944-1G>T is a canonical splice acceptor variant (c.1944-1G>T, intron 12) in SMARCA4, a gene for which loss of function is an established disease mechanism for rhabdoid tumor predisposition syndrome type 2 (RTPS2).

Gene
SMARCA4
Transcript
NM_001128849.1
HGVS · transcript:coding
NM_001128849.1:c.1944-1G>T
Consequence
N/A
GRCh38
chr19:11003339 G>T
GRCh37
chr19:11114015 G>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.1944-1G>T

NM_001128849.1:c.1944-1G>T is a canonical splice acceptor variant (c.1944-1G>T, intron 12) in SMARCA4, a gene for which loss of function is an established disease mechanism for rhabdoid tumor predisposition syndrome type 2 (RTPS2).1 Under the ClinGen SVI PVS1 decision tree (PMC6185798), canonical ±1,2 splice site variants receive PVS1 at very strong strength when LOF is a confirmed disease mechanism. SpliceAI predicts a high-impact splice alteration (delta score 0.99, acceptor loss 0.99), consistent with disruption of the intron 12 splice acceptor.2 The variant is absent from all queried population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the PM2 criterion at moderate strength (<0.1% allele frequency threshold).3 PP3 is not applied because the splice prediction evidence (SpliceAI) is already accounted for in the PVS1 assessment; the ClinGen SVI PVS1 guidance explicitly prohibits stacking PP3 for the same splice-effect evidence.4 Under generic ACMG/AMP 2015 final combination rules (PMID:25741868), PVS1 (Very Strong) plus PM2 (Moderate) yields a classification of Likely Pathogenic.5

PVS1 + PM2 Likely Pathogenic
1 pvs1_gene_contextpvs1_generic_framework ↗
2 pvs1_variant_assessmentspliceai ↗pvs1_generic_framework ↗
4 pvs1_variant_assessment
5 generic_acmg_combination_rules
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 possible splice impact for this variant (max delta score = 0.99). BayesDel score = 0.66.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC