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]
  • See Evidence submitted by expert panel for details.

Variant: NM_000314.7(PTEN):c.254-30dup

CA146028

92817 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: f3d13f7e-dd82-4443-bbf7-33e0fe5e421d
Approved on: 2019-11-22
Published on: 2019-12-04

HGVS expressions

NM_000314.7:c.254-30dup
NM_000314.7(PTEN):c.254-30dup
NC_000010.11:g.87932983dup
CM000672.2:g.87932983dup
NC_000010.10:g.89692740dup
CM000672.1:g.89692740dup
NC_000010.9:g.89682720dup
NG_007466.2:g.74545dup
NM_000314.5:c.254-30dup
NM_000314.6:c.254-30dup
NM_001304717.2:c.773-30dup
NM_001304718.1:c.-497-30dup
NM_001304717.5:c.773-30dup
NM_001304718.2:c.-497-30dup
ENST00000371953.7:c.254-30dup
ENST00000498703.1:n.80-30dup
ENST00000610634.1:c.152-30dup
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Benign

Met criteria codes 1
BA1
Not Met criteria codes 19
PS1 PS3 PS4 PS2 PP2 PP3 PP1 PM2 PM6 PM5 PM4 PM1 BS2 BS1 BS4 PVS1 BP7 BP5 BP2

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.254-30dup (IVS4-30dup) meets criteria to be classified as 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). BA1: Allele frequency of 0.01437 (1.437%, 3748/260,738 alleles) in the gnomAD cohort. (PMID 27535533)
Met criteria codes
BA1
Per our BA1 criteria, gnomAD allele frequency is ≥ 0.01 (1%) in a studied population with ≥2,000 alleles tested and variant present in ≥5 alleles. ExAC, ESP, and 1K allele frequencies are also ≥ 0.01 (1%) .
Not Met criteria codes
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
Variant referred to as c.254-38dupT in paper. Authors characterized PTEN mRNA processing and analyzed PTEN expression. RNA analysis of c.254-38dupT showed no change. PubMed:28677221
PS4
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
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
PM2
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
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
PM1
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
BS1
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
PVS1
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
Curation History
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