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LYFE SCIENCES
Project: HERA
NM_001904.4:c.452G>A
p.Arg151His  ·  CTNNB1
ACMG/AMP
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Classification rationale
1

CTNNB1 NM_001904.4:c.452G>A, p.(Arg151His) is present in gnomAD v4.1 at a total allele frequency of 0.000117726 (190/1613916) with a highest observed population frequency of 0.000154237 in European non-Finnish individuals, both below the non-VCEP PM2 rarity threshold of 0.001 (0.1%), supporting rarity but not absence from population databases.

gnomad_v4 ↗
2

SpliceAI predicts a maximum delta score of 0.02, which is below the splice impact threshold of 0.2 and argues against a splice-disrupting effect.

spliceai ↗
3

ClinVar contains conflicting single-submitter classifications of likely benign and uncertain significance, so this assertion set does not provide decisive classification evidence.

clinvar ↗
4

In the absence of gene-specific criteria, robust case-level enrichment, segregation, de novo, or functional evidence, CTNNB1 p.(Arg151His) is classified as a variant 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
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1This variant is present in gnomAD v2.1 (AF= 3.18573e-05; MAF= 0.00319%, 8/251120 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 7.0466e-05; MAF= 0.00705%, 8/113530 alleles, homozygotes = 0); grpmax FAF= 3.424e-05.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 0.000117726; MAF= 0.01177%, 190/1613916 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000154237; MAF= 0.01542%, 182/1180000 alleles, homozygotes = 0); grpmax FAF= 0.00013971.
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Likely benign (1 clinical laboratory) and as Uncertain significance (1 clinical laboratory).
Functional evidence
03
Functional
OncoKB has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: CTNNB1 (β-catenin), a transcriptional activator, is recurrently mutated in various cancers including endometrial and hepatocellular cancers.
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
COSMIC evidence
05
COSMIC
This variant has previously been reported in somatic cancers (COSMIC; COSV62702481, n = 2 times).
Cancer hotspots evidence
06
Cancer hotspots
No cancer hotspot summary recorded.