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Classification rationale
1

PTEN final classification was assigned using the explicit CSPEC/VCEP criteria-combination framework rather than generic ACMG/AMP combination rules.

2

The applicable pathogenic evidence consists of PS3_Moderate, PM2_Supporting, PP2, and PP3.

3

This combination provides 1 Moderate and 3 Supporting pathogenic criteria, which does not match a defined PTEN rule for Likely Pathogenic or Pathogenic.

4

No benign standalone, strong, or supporting rule combination is satisfied, so the variant remains of uncertain significance.

Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
Rationale
Select a criterion to inspect its explanation.
Evidence used
Gaps remaining
Rule
Publications
Research and evidence
ClinVar evidence
02
ClinVar
This variant is absent from ClinVar.
Functional evidence
03
Functional
OncoKB has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: PTEN, a lipid and protein phosphatase, is one of the most frequently mutated genes in cancer.
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
COSMIC evidence
05
COSMIC
This variant has previously been reported in somatic cancers (COSMIC; COSV64309575, n = 1 times).
Cancer hotspots evidence
06
Cancer hotspots
No cancer hotspot summary recorded.