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NOTCH3
Final classification
VUS
NOTCH3 c.3257A>C · p.Asp1086Ala
NOTCH3

NM_000435.2:c.3257A>C (p.Asp1086Ala) is a missense variant in NOTCH3 exon 20. This variant is absent from large population databases (gnomAD v2.1, v4.1, and gnomAD-Canada; PM2_supporting). No pathogenic or benign criteria beyond PM2_supporting are met. The variant is not cysteine-altering and lies outside known mutational hotspots. No functional, segregation, de novo, case-control, or clinical classification data are available. Based on ACMG/AMP 2015 generic classification rules (PMID:25741868), a single supporting pathogenic criterion (PM2_supporting) is insufficient to reach Likely Pathogenic or any other classification tier. This variant is classified as a Variant of Uncertain Significance (VUS).

Gene
NOTCH3
Transcript
NM_000435.2
HGVS · transcript:coding
NM_000435.2:c.3257A>C
Consequence
N/A
GRCh38
chr19:15180142 T>G
GRCh37
chr19:15290953 T>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; combination = 1 supporting, 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; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
NOTCH3 c.3257A>C

NM_000435.2:c.3257A>C (p.Asp1086Ala) is a missense variant in NOTCH3 exon 20. This variant is absent from large population databases (gnomAD v2.1, v4.1, and gnomAD-Canada; PM2_supporting). No pathogenic or benign criteria beyond PM2_supporting are met. The variant is not cysteine-altering and lies outside known mutational hotspots. No functional, segregation, de novo, case-control, or clinical classification data are available. Based on ACMG/AMP 2015 generic classification rules (PMID:25741868), a single supporting pathogenic criterion (PM2_supporting) is insufficient to reach Likely Pathogenic or any other classification tier. This variant is classified as a Variant of Uncertain Significance (VUS).1

PM2 VUS
1 gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗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 · 1 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 = 0.05). REVEL score = 0.744. BayesDel score = 0.0697656.
      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
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots