Starting
Initialising…
0%
NOTCH2
Final classification
VUS
NOTCH2 c.782T>G · p.Ile261Ser
NOTCH2

NM_024408.3:c.782T>G (p.Ile261Ser) is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (0 alleles), meeting PM2 at supporting strength.

Gene
NOTCH2
Transcript
NM_024408.3
HGVS · transcript:coding
NM_024408.3:c.782T>G
Consequence
N/A
GRCh38
chr1:119987052 A>C
GRCh37
chr1:120529675 A>C
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
NOTCH2 c.782T>G

NM_024408.3:c.782T>G (p.Ile261Ser) is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (0 alleles), meeting PM2 at supporting strength.1 This variant has been reported in ClinVar (Variation ID 591665) as Uncertain significance by a single clinical testing laboratory (Labcorp Genetics, criteria provided, single submitter); no submitter has classified it as pathogenic or benign.2 No published functional studies, de novo observations, case-control enrichment, or family segregation data exist for this specific variant.3 In silico predictions are discordant: REVEL (0.80) supports a deleterious effect while BayesDel (0.402) does not; SpliceAI predicts no splicing impact (max delta 0.02). Neither PP3 nor BP4 can be applied.4 PVS1 is not applicable as this is a missense variant outside the null-variant buckets defined by ClinGen SVI PVS1 recommendations (PMC6185798).5 The only applicable criterion is PM2 (supporting); one supporting pathogenic criterion is insufficient to classify this variant above Variant of Uncertain Significance per ACMG/AMP 2015 combination rules.6

PM2 VUS
4 revelbayesdelspliceai ↗
5 pvs1_generic_framework ↗pvs1_variant_assessment
6 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 · 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
      Population frequency
      Absent from gnomAD v4.1.
      Absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 591665)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.8. BayesDel score = 0.401803.
      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.
      Literature · 2 PMIDs triaged · 1 high-priority
      2papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      25741868 ↗ functional
      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.
      The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic
      BS3PP5PS3PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots