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

Variant: NM_000314.7(PTEN):c.-801G>A

CA10577405

234695 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 860ec6b0-d335-4837-b1b8-0bee56a51524
Approved on: 2020-10-20
Published on: 2022-09-30

HGVS expressions

NM_000314.7:c.-801G>A
NM_000314.7(PTEN):c.-801G>A
NC_000010.11:g.87863668G>A
CM000672.2:g.87863668G>A
NC_000010.10:g.89623425G>A
CM000672.1:g.89623425G>A
NC_000010.9:g.89613405G>A
NG_007466.2:g.5231G>A
NG_033079.1:g.4770C>T
ENST00000688158.1:c.-802G>A
ENST00000688308.1:c.-17+555G>A
ENST00000693560.1:c.-282G>A
ENST00000371953.8:c.-802G>A
ENST00000371953.7:c.-802G>A
ENST00000610634.1:c.-904G>A
NM_000314.5:c.-801G>A
NM_000314.6:c.-801G>A
NM_001304717.2:c.-282G>A
NM_001304718.1:c.-1506G>A
NM_001304717.5:c.-282G>A
NM_001304718.2:c.-1506G>A
NM_000314.8:c.-802G>A
NM_000314.8(PTEN):c.-802G>A

Uncertain Significance

Met criteria codes 1
PM2
Not Met criteria codes 25
PVS1 BA1 BS4 BS3 BS1 BS2 BP5 BP7 BP2 BP3 BP4 BP1 PS2 PS4 PS3 PS1 PP4 PP1 PP3 PP2 PM3 PM1 PM4 PM5 PM6

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.-802G>A, also described as c.-801G>A (NC_000010.11:g.87863668G>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
Met criteria codes
PM2
Variant not present in gnomAD (version 3.0).
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
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
BS1
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
Gene Dx internal data: Several cancer panel cases, all with breast cancer. Two with PATH co-occurrences in other breast genes (BRCA2, ATM) but too much PTEN overlap for BP5. Nobody homozygous or anything else that gets criteria.
BP7
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
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
Gene Dx internal lab data: several cases picked up on panels with no helpful info, no co-occurrences, no segregation data
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
PP2
Promotor variant
PM3
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
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
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