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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
      Population frequency
      Overall AF
      1 / 1,602,340
      6.2e-05%
      Highest · African/African American
      0.0013%
      Homozygotes
      0
      Allele frequency by ancestry — gnomAD v4.1
      observed in 1 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      African/African American 1 / 74,766 0.0013% 0
      Admixed American 0 / 59,760
      European (Finnish) 0 / 62,658
      Amish 0 / 912
      East Asian 0 / 44,618
      Middle Eastern 0 / 5,026
      South Asian 0 / 90,744
      Ashkenazi Jewish 0 / 29,444
      European (non-Finnish) 0 / 1,172,636
      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).
      Overall AF
      Not observed
      Homozygotes
      0
      Not observed in any ancestry group across 8 populations in gnomAD 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).
      This variant is absent from gnomAD-Canada.
      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