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]
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Variant: NM_000314.6(PTEN):c.-1170C>T

CA151481

127662 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 8c50af60-fe53-4c9b-b60a-3735d21c8645
Approved on: 2020-03-23
Published on: 2020-03-26

HGVS expressions

NM_000314.6:c.-1170C>T
NM_000314.6(PTEN):c.-1170C>T
NC_000010.11:g.87863299C>T
CM000672.2:g.87863299C>T
NC_000010.10:g.89623056C>T
CM000672.1:g.89623056C>T
NC_000010.9:g.89613036C>T
NG_007466.2:g.4862C>T
NG_033079.1:g.5139G>A
ENST00000706954.1:c.-17+657C>T
ENST00000688308.1:c.-17+186C>T
ENST00000445946.5:c.-812G>A
ENST00000371953.7:c.-1171C>T
ENST00000445946.3:c.-812G>A
NM_001126049.1:c.-812G>A
NM_001126049.2:c.-812G>A
More

Likely Benign

Met criteria codes 2
BS1_Supporting BP5
Not Met criteria codes 23
PP1 PP2 PP3 PP4 PM1 PM3 PM5 PM4 PM6 PM2 BA1 BS2 BS4 BS3 PS1 PS2 PS3 PS4 BP7 BP4 BP3 BP1 BP2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.-1170C>T (NC_000010.10:g. 89623056C>T) meets criteria to be classified as likely benign 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 0.0002477 (0.02477%, 16/64,586 alleles) in the European subpopulation of the gnomAD cohort. (PMID 27535533) BP5: Variant found in multiple cases with alternate molecular basis for disease. (Internal laboratory contributor(s) SCV000149466.6, SCV000184146.1)
Met criteria codes
BS1_Supporting
present in 16/64586 (0.02477%) European alleles in gnomAD V3
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
PP1
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
PP4
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
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
PM4
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
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
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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
EP reviewed Wang 2011, decided not relevant for criteria application.
PS4
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
BP4
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
BP1
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
Curation History
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