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SMARCA4
Final classification
Likely Benign
SMARCA4 c.3894C>T · p.Asp1298=
SMARCA4

NM_001128849.3:c.3894C>T is a synonymous variant (p.Asp1298=) in the SMARCA4 gene. Synonymous variants that do not alter splicing are typically benign.

Gene
SMARCA4
Transcript
NM_001128849.3
HGVS · transcript:coding
NM_001128849.3:c.3894C>T
Consequence
N/A
GRCh38
chr19:11034143 C>T
GRCh37
chr19:11144819 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: BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; combination = 3 supporting benign, which maps to Likely Benign.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; combination = 3 supporting benign, which maps to Likely Benign.
Classification rationale
BP4BP6BP7 Likely Benign
SMARCA4 c.3894C>T

NM_001128849.3:c.3894C>T is a synonymous variant (p.Asp1298=) in the SMARCA4 gene. Synonymous variants that do not alter splicing are typically benign.1 This variant is present in population databases at very low frequencies: gnomAD v2.1 (12/251,084 alleles, AF=0.0048%), gnomAD v4.1 (60/1,613,590 alleles, AF=0.0037%), and gnomAD-Canada (9/18,414 alleles, AF=0.049%). Population frequency alone is insufficient to classify this variant as benign or pathogenic by allele frequency thresholds.2 SpliceAI predicts no significant impact on splicing (max delta score 0.03), and the synonymous nucleotide substitution is not predicted to create or disrupt a splice site. This supports a benign interpretation under both BP4 and BP7.3 This variant has been reported in ClinVar as Likely benign by six clinical laboratories (ClinVar Variation ID: 238439). No laboratory has submitted a conflicting classification, supporting BP6.4 No published literature was identified that specifically describes NM_001128849.3:c.3894C>T. All PMIDs associated with ClinVar submissions refer to methodological or guideline publications that do not mention this variant. Applying generic ACMG/AMP 2015 combination rules (Richards et al., PMID:25741868): three supporting benign criteria are met (BP4, BP6, BP7) with no pathogenic criteria met. The combination of two or more supporting benign criteria is sufficient for a classification of Likely Benign.5

BP4 + BP6 + BP7 Likely Benign
Gene diagram · NM_001128849.3 · variants mapped to exon structure
SMARCA4 NM_001128849.3
Fetching transcript structure from UCSC…
Applied criteria · 3 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 benign
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 3.71842e-05; MAF= 0.00372%, 60/1613590 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 4.83092e-05; MAF= 0.00483%, 57/1179900 alleles, homozygotes = 0); grpmax FAF= 3.775e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 4.77928e-05; MAF= 0.00478%, 12/251084 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000108767; MAF= 0.01088%, 2/18388 alleles, homozygotes = 0); grpmax FAF= 4.747e-05.
      🇨🇦 CA
      This variant is present in gnomAD-Canada v1.0 (AF= 0.0004887585532746823, 9/18414 alleles, homozygotes = 0).
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0037% · 60 / 1,613,590
      0 hom · FAF 0.0038%
      European (non-Finnish)
      57 / 1,179,900
      0.0048%
      East Asian
      2 / 44,900
      0.0045%
      Remaining individuals
      1 / 62,484
      0.0016%
      + 7 not observed (Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0048% · 12 / 251,084
      0 hom · FAF 0.0047%
      East Asian
      2 / 18,388
      0.011%
      European (non-Finnish)
      10 / 113,440
      0.0088%
      + 6 not observed (African/African American, Admixed American, Ashkenazi Jewish, European (Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      0.049% · 9 / 18,414
      0 hom · FAF 0.034%
      Remaining individuals
      1 / 1,138
      0.088%
      European (non-Finnish)
      8 / 11,736
      0.068%
      + 7 not observed (African/African American, Latino/Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, South Asian)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (6 clinical laboratories). (ClinVarID = 238439)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
      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.
      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
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      29215836 ↗ Rhabdoid Tumor Predisposition Syndrome. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR