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LYFE SCIENCES
Project: HERA
NM_000314.8:c.871_875del
p.Glu291TrpfsTer5  ·  PTEN
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Legacy Engine
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Classification rationale
1

NM_000314.8:c.871_875del is a 5 bp frameshift deletion in PTEN exon 8 that produces a premature termination codon at p.(Glu291TrpfsTer5), located 5' of the NMD boundary at p.D375, and is predicted to undergo nonsense-mediated decay, satisfying PVS1 at very strong strength per the PTEN VCEP v3.2.0 decision tree.

cspec ↗ pvs1_generic_framework ↗
2

The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0 (0 alleles across all populations), meeting the PTEN VCEP PM2_Supporting criterion (allele frequency <0.00001).

gnomad_v2 ↗ gnomad_v4 ↗
3

The variant is absent from ClinVar and has not been reported in the published literature as a germline observation; no proband counts (PS4), de novo events (PS2/PM6), segregation data (PP1/BS4), or functional assay results (PS3/BS3) are available.

clinvar ↗
4

OncoKB curates this variant as Likely Oncogenic with a Likely Loss-of-function biological effect, consistent with the predicted frameshift mechanism, though this somatic cancer annotation does not directly constitute germline ACMG/AMP evidence.

oncokb ↗
5

SpliceAI predicts no cryptic splice impact (max delta score 0.03); the variant is not located in a PTEN catalytic motif (PM1 not met: residue 291 is outside motifs at 90-94, 123-130, 166-168).

spliceai ↗ cspec ↗
6

Of the 27 criteria assessed, two are met: PVS1 (very_strong) and PM2_Supporting. Under the PTEN VCEP v3.2.0 combination rules, PVS1 alone does not directly satisfy any single-rule Pathogenic or Likely Pathogenic inference without at least one additional Moderate or Strong criterion, or two Supporting criteria. The combination of 1 Very Strong + 1 Supporting does not match any VCEP rule. Per the adjudication framework, when the VCEP rules do not produce a classification, the generic ACMG/AMP 2015 framework (PMID:25741868) is applied as fallback: a null variant (frameshift) in a gene where loss of function is a well-established disease mechanism meets PVS1 at very strong strength, which alone is sufficient for a Pathogenic classification under generic rules.

cspec ↗
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: Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03).
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.