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NOTCH2
Final classification
VUS
NOTCH2 c.3570G>C · p.Glu1190Asp
NOTCH2

NM_024408.3:c.3570G>C (p.Glu1190Asp) in NOTCH2 is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, supporting a rare variant interpretation.

Gene
NOTCH2
Transcript
NM_024408.3
HGVS · transcript:coding
NM_024408.3:c.3570G>C
Consequence
N/A
GRCh38
chr1:119935557 C>G
GRCh37
chr1:120478180 C>G
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
NOTCH2 c.3570G>C

NM_024408.3:c.3570G>C (p.Glu1190Asp) in NOTCH2 is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, supporting a rare variant interpretation.1 Multiple in silico predictors suggest no significant impact: BayesDel predicts a benign score (-0.045) and SpliceAI indicates no splicing impact (max delta 0.07).2 The variant is a novel missense change at a residue not in a known functional domain or mutational hotspot. No functional studies, segregation data, or de novo reports are available.3 Applying generic ACMG/AMP 2015 combination rules: PM2 (supporting pathogenic) and BP4 (supporting benign) are both met. The single supporting pathogenic and single supporting benign criterion do not reach the threshold for Likely Pathogenic or Likely Benign.4 This variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 + BP4 VUS
2 bayesdelspliceai ↗
4 generic_acmg_combination_rules
5 generic_acmg_combination_rules
Gene diagram · NM_024408.3 · variants mapped to exon structure
NOTCH2 NM_024408.3
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
      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 no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.567. BayesDel score = -0.0446258.
      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. NOTCH2 encodes a transmembrane receptor that regulates many aspects of development by affecting cell-fate determination.
      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