Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
Link to SEPIO compliant JSON-LD document
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!

Variant: NM_000546.5(TP53):c.28G>A (p.Val10Ile)

CA000093

127806 (ClinVar)

Gene: TP53
Condition: Li-Fraumeni syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 48c832f0-7992-455f-bf7e-15572c0d545d
Approved on: 2024-08-05
Published on: 2024-08-05

HGVS expressions

NM_000546.5:c.28G>A
NM_000546.5(TP53):c.28G>A (p.Val10Ile)
NC_000017.11:g.7676567C>T
CM000679.2:g.7676567C>T
NC_000017.10:g.7579885C>T
CM000679.1:g.7579885C>T
NC_000017.9:g.7520610C>T
NG_017013.2:g.15984G>A
ENST00000503591.2:c.28G>A
ENST00000508793.6:c.28G>A
ENST00000509690.6:c.-21-1331G>A
ENST00000514944.6:c.28G>A
ENST00000604348.6:c.28G>A
ENST00000269305.9:c.28G>A
ENST00000269305.8:c.28G>A
ENST00000359597.8:c.28G>A
ENST00000413465.6:c.28G>A
ENST00000420246.6:c.28G>A
ENST00000445888.6:c.28G>A
ENST00000455263.6:c.28G>A
ENST00000503591.1:c.28G>A
ENST00000505014.5:n.167G>A
ENST00000508793.5:c.28G>A
ENST00000509690.5:c.-21-1331G>A
ENST00000514944.5:c.28G>A
ENST00000604348.5:c.28G>A
ENST00000610292.4:c.-207G>A
ENST00000610538.4:c.-90G>A
ENST00000615910.4:c.28G>A
ENST00000617185.4:c.28G>A
ENST00000619485.4:c.-90G>A
ENST00000620739.4:c.-90G>A
ENST00000622645.4:c.-90G>A
ENST00000635293.1:c.-90G>A
NM_001126112.2:c.28G>A
NM_001126113.2:c.28G>A
NM_001126114.2:c.28G>A
NM_001126118.1:c.-207G>A
NM_001276695.1:c.-90G>A
NM_001276696.1:c.-90G>A
NM_001276760.1:c.-90G>A
NM_001276761.1:c.-90G>A
NM_001276695.2:c.-90G>A
NM_001276696.2:c.-90G>A
NM_001276760.2:c.-90G>A
NM_001276761.2:c.-90G>A
NM_000546.6:c.28G>A
NM_001126112.3:c.28G>A
NM_001126113.3:c.28G>A
NM_001126114.3:c.28G>A
NM_001126118.2:c.-207G>A
NM_001276695.3:c.-90G>A
NM_001276696.3:c.-90G>A
NM_001276760.3:c.-90G>A
NM_001276761.3:c.-90G>A

Benign

Met criteria codes 4
BS3 BS2 BP4 PM2_Supporting
Not Met criteria codes 11
BA1 PP4 PP1 PP3 PM1 PM5 BS4 BS1 PS2 PS4 PS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TP53 Version 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
TP53 VCEP
The NM_000546.6: c.28G>A variant in TP53 is a missense variant predicted to cause substitution of Valine by Isoleucine at amino acid 10 (p.Val10Ile). This variant has been observed in at least 8 heterozygous unrelated females from the same data source with no personal history of cancer prior to age 60 years and no personal history of sarcoma at any age (BS2; Internal lab contributors: SCV000184102.7). This variant has an allele frequency of .000021066 (34/1613962 alleles) across gnomAD v4.1.0 (after removing low AB alleles likely to represent CHIP contamination and recalculating total allele frequency) which is lower than the Clingen TP53 VCEP threshold (<0.00003) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). In vitro assays performed in yeast and/or human cell lines showed functional transactivation and retained growth suppression activity indicating that this variant does not impact protein function (BS3; PMIDs: 12826609, 29979965, 30224644). Computational predictor scores (BayesDel = -0.0961; Align GVGD Class C0) are below the recommended thresholds (BayesDel ≤ -0.008 and an Align GVGD Class ≤ 55), evidence that does not predict a damaging effect on TP53 via protein change. SpliceAI predicts that the variant has no impact on splicing (BP4_Moderate). In summary, this variant meets the criteria to be classified as Benign for Li Fraumeni Syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen TP53 VCEP: BS2, PM2_Supporting, BS3, BP4_moderate. (Bayesian Points: -9; VCEP specifications version 2.0; 7/24/2024).
Met criteria codes
BS3
In vitro assays performed in yeast and/or human cell lines showed functional transactivation and retained growth suppression activity indicating that this variant does not impact protein function (BS3; PMIDs: 12826609, 29979965, 30224644).
BS2
This variant has been observed in at least 8 heterozygous unrelated females from the same data source with no personal history of cancer prior to age 60 years and no personal history of sarcoma at any age (BS2; Internal lab contributors: SCV000184102.7).
BP4
BP4_MODERATE Computational predictor scores (BayesDel = -0.0961; Align GVGD Class C0) are below the recommended thresholds (BayesDel ≤ -0.008 and an Align GVGD Class ≤ 55), evidence that does not predict a damaging effect on TP53 via protein change. SpliceAI predicts that the variant has no impact on splicing (BP4_Moderate)
PM2_Supporting
This variant has an allele frequency of .000021066 (34/1613962 alleles) across gnomAD v4.1.0 (after removing low AB alleles likely to represent CHIP contamination and recalculating total allele frequency) which is lower than the Clingen TP53 VCEP threshold (<0.00003) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting).
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
This variant does not reside within a region of TP53 that is defined as a mutational hotspot by the ClinGen TP53 VCEP (PM1 not met).
PM5
3 different missense variants with equal or lesser impact (c.29T>G, p.Val10Gly; c.28G>T, p.Val1-Phe; c.28G>C, p.Val10Leu) in the same codon have been reported (ClinVar Variation IDs: 822501, 968647, 231387). However, these variants have not yet been curated to determine if they would be classified as pathogenic or likely pathogenic by the ClinGen TP53 VCEP’s specifications (PM5 not evaluated).
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
Bring to Experts: V3.1.2 has AF of 0.0004960 in Other subpop - does this count?
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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