Variant: NM_000314.7(PTEN):c.-834C>T

CA000602

127676 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

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: BS1_Supporting

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

Expert Panel

PTEN VCEP

Criteria Specification Information

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

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

• BA1: 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
• 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
• PVS1: 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
• 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
• 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.