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.-834C>T

CA000602

127676 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: a132ee62-ecee-493a-9e46-a437c8953e66
Approved on: 2020-10-20
Published on: 2022-09-30

HGVS expressions

NM_000314.7:c.-834C>T
NM_000314.7(PTEN):c.-834C>T
NC_000010.11:g.87863635C>T
CM000672.2:g.87863635C>T
NC_000010.10:g.89623392C>T
CM000672.1:g.89623392C>T
NC_000010.9:g.89613372C>T
NG_007466.2:g.5198C>T
NG_033079.1:g.4803G>A
ENST00000688158.1:c.-835C>T
ENST00000688308.1:c.-17+522C>T
ENST00000692337.1:n.77C>T
ENST00000693560.1:c.-315C>T
ENST00000371953.8:c.-835C>T
ENST00000371953.7:c.-835C>T
ENST00000610634.1:c.-937C>T
NM_000314.5:c.-834C>T
NM_000314.6:c.-834C>T
NM_001304717.2:c.-315C>T
NM_001304718.1:c.-1539C>T
NM_001304717.5:c.-315C>T
NM_001304718.2:c.-1539C>T
NM_000314.8:c.-835C>T
NM_000314.8(PTEN):c.-835C>T

Uncertain Significance

Met criteria codes 1
BS1_Supporting
Not Met criteria codes 23
BS2 BS4 BP5 BP7 BP2 BP3 BP4 BP1 PS4 PS2 PS1 BA1 PP4 PP1 PP3 PP2 PM3 PM1 PM4 PM5 PM6 PM2 PVS1

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.-835C>T, also described as c.-834C>T (NC_000010.10:g.89623392C>T) 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). BS1_P: Allele frequency of 0.0002207 (0.02207%, 15/67980 alleles) in the European subpopulation of the gnomAD cohort, v3.1.2. (PMID 27535533)
Met criteria codes
BS1_Supporting
gnomAD data.
Not Met criteria codes
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
BP5
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
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
PS4
At this time, the highest calculated adult CC score = 5 from details provided in the papers.
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
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
PP2
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
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
PM2
1 allele present in gnomAD with allele frequency of ~0.00003.
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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