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
  • See Evidence submitted by expert panel for details.

Variant: NM_000314.7(PTEN):c.802-3T>A

CA000593

135912 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: aa1070f5-4e74-49ed-a3cd-9f7d0c2d5a35
Approved on: 2020-03-23
Published on: 2020-03-25

HGVS expressions

NM_000314.7:c.802-3T>A
NM_000314.7(PTEN):c.802-3T>A
NC_000010.11:g.87960891T>A
CM000672.2:g.87960891T>A
NC_000010.10:g.89720648T>A
CM000672.1:g.89720648T>A
NC_000010.9:g.89710628T>A
NG_007466.2:g.102453T>A
NM_000314.5:c.802-3T>A
NM_000314.6:c.802-3T>A
NM_001304717.2:c.1321-3T>A
NM_001304718.1:c.211-3T>A
NM_001304717.5:c.1321-3T>A
NM_001304718.2:c.211-3T>A
NM_000314.8:c.802-3T>A
ENST00000371953.7:c.802-3T>A
ENST00000472832.2:n.229-3T>A

Uncertain Significance

Met criteria codes 2
BP4 PM2
Not Met criteria codes 20
BS1 BS3 BS4 BS2 BP7 BP5 BP2 PVS1 PS3 PS4 PS2 PS1 PP2 PP3 PP1 PM4 PM1 PM5 PM6 BA1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.802-3T>A (IVS7-3T>A) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PM2: Absent in large sequenced populations BP4: Intronic variant where at least 2 out of 3 in silico models predict no splicing impact.
Met criteria codes
BP4
VCEP agreed that minimal impact observed using HSF (-1.92%) and lack of cryptic would be considered no impact (NNSplice also no impact, MaxEnt native site weakened)
PM2
Variant is absent in population databases.
Not Met criteria codes
BS1
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
BS4
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
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
BP2
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
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
1 internal case: female with ILC breast ca in 40s; her family history includes mother breast/uterine/bladder cancers dx 70s-80s; mat uncle pancreatic ca in 80s; mat aunt breast ca in 60s; father lung ca in 70s; CC score = 2.
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
PP2
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
PP1
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
PM1
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
PM6
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
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