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NOTCH3
Final classification
VUS
NOTCH3 c.4688C>T · p.Pro1563Leu
NOTCH3

NM_000435.2:c.4688C>T (p.Pro1563Leu) is a missense variant in NOTCH3. It is absent from gnomAD v2.1 (0/242,354 alleles) and ultra-rare in gnomAD v4.1 (1/1,602,340 alleles; AF=6.24e-7), meeting PM2_Supporting.

Gene
NOTCH3
Transcript
NM_000435.2
HGVS · transcript:coding
NM_000435.2:c.4688C>T
Consequence
N/A
GRCh38
chr19:15174116 G>A
GRCh37
chr19:15284927 G>A
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: PM2 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
NOTCH3 c.4688C>T

NM_000435.2:c.4688C>T (p.Pro1563Leu) is a missense variant in NOTCH3. It is absent from gnomAD v2.1 (0/242,354 alleles) and ultra-rare in gnomAD v4.1 (1/1,602,340 alleles; AF=6.24e-7), meeting PM2_Supporting.1 Multiple computational predictors indicate a benign impact: REVEL score 0.08, BayesDel score -0.37, and SpliceAI max delta 0.00. This meets BP4 (supporting benign).2 The variant is a missense substitution (not a null variant), so PVS1 is not applicable. It alters a non-cysteine residue (Pro1563) in EGF-like repeat 30, where the majority of established pathogenic NOTCH3 variants affect conserved cysteine residues; PM1 is not met.3 The variant is absent from ClinVar and has no reported functional studies, de novo observations, case-control data, or family segregation data. OncoKB classifies it as 'Unknown Oncogenic Effect.'4 In the generic ACMG/AMP 2015 framework, the current evidence yields PM2_Supporting and BP4_Supporting_Benign. These criteria are insufficient for a definitive classification; the variant remains a Variant of Uncertain Significance (VUS) pending additional clinical and functional data.5

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
3 pvs1_variant_assessmentpvs1_generic_framework ↗
5 generic_acmg_combination_rules
Gene diagram · NM_000435.2 · variants mapped to exon structure
NOTCH3 NM_000435.2
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
      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= 6.24087e-07; MAF= 0.00006%, 1/1602340 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.33751e-05; MAF= 0.00134%, 1/74766 alleles, homozygotes = 0).
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/242354 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/15004 alleles, homozygotes = 0).
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,602,340
      0 hom
      African/African American
      1 / 74,766
      0.0013%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, European (non-Finnish))
      gnomAD v2.1
      Absent · 0 / 242,354
      0 hom
      Not observed in any ancestry group.
      + 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
      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 = 0.00). REVEL score = 0.08. BayesDel score = -0.370843.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. NOTCH3 encodes a Type I transmembrane protein of the Notch family. Missense and nonsense mutations in NOTCH3 have been identified in various cancers.
      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
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots