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LYFE SCIENCES
Project: HERA
NM_006218.4:c.2782C>T
p.Gln928Ter  ·  PIK3CA
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Classification rationale
1

The PIK3CA c.2782C>T (p.Gln928Ter; p.Q928*) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar.

cosmic ↗ clinvar ↗
2

This variant is absent from gnomAD v2.1 and gnomAD v4.1, which is within the Brain Malformations VCEP PM2_Supporting threshold of at most 1 occurrence in population data and below the BS1 (>0.0185%) and BA1 (>0.0926%) thresholds.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

The variant lies within the PIK3CA kinase domain approved for PM1_Supporting by the Brain Malformations VCEP (amino acids 797-1068), supporting location in a critical functional region.

cspec ↗
4

SpliceAI predicts no significant splice impact for this variant with a maximum delta score of 0.10, although PP3 and BP4 are not applicable to this nonsense variant under the Brain Malformations VCEP specifications.

spliceai ↗ 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
PS1
—
—
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.
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Unknown Oncogenic Effect
OncoKB oncogenicity for this specific variant: Unknown Oncogenic Effect (variant has not been individually curated).
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.10).
SpliceAI ↗
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).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueQ928
Hotspots ↗