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SMARCA4
Final classification
Likely Pathogenic
SMARCA4 c.1813-2A>T · p.?
SMARCA4

NM_001128849.1:c.1813-2A>T is a canonical splice acceptor variant at position -2 in SMARCA4, a gene where loss of function is an established germline disease mechanism causing rhabdoid tumor predisposition syndrome type 2 (RTPS2) and small cell carcinoma of the ovary hypercalcemic type (SCCOHT) [PVS1, very strong].

Gene
SMARCA4
Transcript
NM_001128849.1
HGVS · transcript:coding
NM_001128849.1:c.1813-2A>T
Consequence
N/A
GRCh38
chr19:11003027 A>T
GRCh37
chr19:11113703 A>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.1813-2A>T

NM_001128849.1:c.1813-2A>T is a canonical splice acceptor variant at position -2 in SMARCA4, a gene where loss of function is an established germline disease mechanism causing rhabdoid tumor predisposition syndrome type 2 (RTPS2) and small cell carcinoma of the ovary hypercalcemic type (SCCOHT) [PVS1, very strong].1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (allele frequency = 0%), consistent with PM2 at moderate strength under generic ACMG/AMP 2015 criteria.2 SpliceAI predicts a strong splice-disrupting effect (max delta = 1.0; DS_AL=1.0, DS_AG=0.89) and BayesDel predicts a damaging score (0.66), but PP3 is not stacked with PVS1 per ClinGen SVI guidance (PMC6185798) to avoid double-counting the same splice-effect evidence.3 This variant is absent from ClinVar and has not been reported in any publication; no external classification, functional data, segregation data, or de novo observations are available.4 Under generic ACMG/AMP 2015 combination rules, one very strong (PVS1) and one moderate (PM2) criterion are sufficient for a Pathogenic classification. However, transcript version discrepancy (NM_001128849.1 vs NM_001128849.3) and absence of RNA-confirmed splicing impact warrant confirmatory review.5

PVS1 + PM2 Likely Pathogenic
1 pvs1_generic_framework ↗pvs1_gene_contextpvs1_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 = 1.00). 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