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LYFE SCIENCES
Project: HERA
NM_000546.5:c.344A>G
p.His115Arg  ·  TP53
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Classification rationale
1

The TP53 c.344A>G (p.His115Arg) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar, where the ClinGen TP53 Variant Curation Expert Panel classifies it as Likely Benign.

clinvar ↗
2

This variant is absent from gnomAD v2.1 and gnomAD v4.1, which is below the TP53 VCEP PM2_Supporting threshold of less than 0.00003 and supports rarity in population databases.

cspec ↗ gnomad_v2 ↗ gnomad_v4 ↗
3

In TP53 functional studies summarized by the TP53 VCEP functional worksheet, p.His115Arg was functional in Kato data and showed no loss of function in Giacomelli and Kotler data, supporting BS3.

PMID:12826609 ↗ PMID:29979965 ↗
4

TP53-specific in silico assessment assigns BP4 because BayesDel is 0.0464313, below the TP53 PP3 threshold of 0.16, and SpliceAI predicts no meaningful splice effect with a maximum delta score of 0.03 below the 0.2 threshold; REVEL is 0.484.

spliceai ↗
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
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Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
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Research and evidence
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories) and as Likely benign (2 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Likely Benign by ClinGen TP53 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 182925)
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.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.484. BayesDel score = 0.0464313.
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.
ResidueH115
Hotspots ↗