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_000314.7(PTEN):c.159A>G (p.Val53=)

CA000127

184020 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 995c0e99-dc70-494f-bb25-ccabe14633fb
Approved on: 2024-02-09
Published on: 2024-03-04

HGVS expressions

NM_000314.7:c.159A>G
NM_000314.7(PTEN):c.159A>G (p.Val53=)
NC_000010.11:g.87894104A>G
CM000672.2:g.87894104A>G
NC_000010.10:g.89653861A>G
CM000672.1:g.89653861A>G
NC_000010.9:g.89643841A>G
NG_007466.2:g.35666A>G
ENST00000700029.2:c.159A>G
ENST00000710265.1:c.159A>G
ENST00000472832.3:c.159A>G
ENST00000688158.2:n.899+13666A>G
ENST00000688922.2:c.159A>G
ENST00000700021.1:c.159A>G
ENST00000700022.1:c.159A>G
ENST00000706954.1:c.159A>G
ENST00000706955.1:c.*194A>G
ENST00000686459.1:c.159A>G
ENST00000688158.1:c.*275+13666A>G
ENST00000688308.1:c.159A>G
ENST00000688922.1:c.28A>G
ENST00000693560.1:c.678A>G
ENST00000371953.8:c.159A>G
ENST00000371953.7:c.159A>G
ENST00000462694.1:n.161A>G
ENST00000610634.1:c.57A>G
NM_000314.5:c.159A>G
NM_000314.6:c.159A>G
NM_001304717.2:c.678A>G
NM_001304718.1:c.-547A>G
NM_001304717.5:c.678A>G
NM_001304718.2:c.-547A>G
NM_000314.8:c.159A>G
NM_000314.8(PTEN):c.159A>G (p.Val53=)
More

Likely Benign

Met criteria codes 2
BS1_Supporting BP4
Not Met criteria codes 24
PS4 PS2 PS1 PS3 PP4 PP1 PP3 PP2 PM5 PM1 PM4 PM3 PM6 PM2 BA1 PVS1 BS4 BS3 BS2 BP5 BP7 BP3 BP2 BP1

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.159A>G (p.Val53=) 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_P: To be applied for variants with filtering allele frequency of 0.0000043 up to 0.000043 (0.00043% up to 0.0043%) in gnomAD. Popmax FAF of this variant=0.00004593 (9 alleles v4 gnomAD). BP4: Synonymous variant where SpliceAI model predict no splicing impact (acceptor gain 0.08, donor gain 0.13).
Met criteria codes
BS1_Supporting
To be applied for variants with filtering allele frequency of 0.0000043 up to 0.000043 (0.00043% up to 0.0043%) in gnomAD. Popmax FAF of this variant=0.00004593 (9 alleles v4 gnomAD).
BP4
Synonymous variant where SpliceAI model predict no splicing impact (acceptor gain 0.08, donor gain 0.13).
Not Met criteria codes
PS4
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
PS1
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
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
In silico models (HSF, FF, MaxEnt) predict no deleterious impact on the native donor; however, MaxEnt and HSF predict an alternate donor site 5 NT upstream is strengthened.
PP2
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
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
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
PVS1
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
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
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
In silico models (MaxEnt and HSF) predict an alternate donor site will be strengthened.
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
Curation History
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