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]

Variant: NM_000314.8(PTEN):c.882T>G (p.Ser294Arg)

CA000618

127693 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: ea71ad62-785a-426a-b9bd-7ffff8b8a049
Approved on: 2023-08-04
Published on: 2023-10-19

HGVS expressions

NM_000314.8:c.882T>G
NM_000314.8(PTEN):c.882T>G (p.Ser294Arg)
NC_000010.11:g.87960974T>G
CM000672.2:g.87960974T>G
NC_000010.10:g.89720731T>G
CM000672.1:g.89720731T>G
NC_000010.9:g.89710711T>G
NG_007466.2:g.102536T>G
ENST00000686459.1:c.*468T>G
ENST00000688158.1:c.*993T>G
ENST00000688308.1:c.882T>G
ENST00000688922.1:c.803T>G
ENST00000693560.1:c.1401T>G
ENST00000371953.8:c.882T>G
ENST00000371953.7:c.882T>G
ENST00000472832.2:c.309T>G
NM_000314.5:c.882T>G
NM_000314.6:c.882T>G
NM_001304717.2:c.1401T>G
NM_001304718.1:c.291T>G
NM_000314.7:c.882T>G
NM_001304717.5:c.1401T>G
NM_001304718.2:c.291T>G
More

Likely Benign

Met criteria codes 3
PP2 BS1 BP4
Not Met criteria codes 23
PVS1 BA1 PS2 PS4 PS3 PS1 PP4 PP1 PP3 PM6 PM2 PM1 PM4 PM3 PM5 BS2 BS4 BS3 BP3 BP2 BP1 BP7 BP5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
NM_000314.8(PTEN):c.882T>G (p.Ser294Arg) meets criteria to be classified as likely benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.0.0). Please see a summary of the rules and criteria codes in the 'PTEN ACMG Specifications Summary' document (assertion method column). BS1: Filtering allele frequency of 0.0002887 (0.02887%, 13/24922 African/African American alleles) in gnomAD. BP4: REVEL score = 0.365. PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. Variant with benign and pathogenic codes. Classification based on application of Bayesian Classification Framework (PMID: 29300386): BS1 (-4 pts), BP4 (-1 pt), PP2 (+1 pt) = -4 pts total (Likely Benign).
Met criteria codes
PP2
PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
BS1
Popmax FAF exome (0.0002887 [0.02887%]) within BS1 thresholds (0.0043% - 0.056%)
BP4
REVEL score = 0.365 (<0.5 threshold)
Not Met criteria codes
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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
PS3
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
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
JM agree
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
Low confidence of cumulative score per Mighell. Variant found in Matreyek supplemental table. Considered WT-like with protein abundance score of 0.92. Per EP, BS3 not to be applied if Mighell low confidence and Matreyek is only other evidence.
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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