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]

Variant: NM_000314.8(PTEN):c.577C>T (p.Leu193=)

CA060268

481156 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: ce1a23aa-e2da-4ad0-a263-4420d1a003a1
Approved on: 2021-06-04
Published on: 2022-09-30

HGVS expressions

NM_000314.8:c.577C>T
NM_000314.8(PTEN):c.577C>T (p.Leu193=)
NC_000010.11:g.87952202C>T
CM000672.2:g.87952202C>T
NC_000010.10:g.89711959C>T
CM000672.1:g.89711959C>T
NC_000010.9:g.89701939C>T
NG_007466.2:g.93764C>T
ENST00000686459.1:c.*163C>T
ENST00000688158.1:c.*688C>T
ENST00000688308.1:c.577C>T
ENST00000688922.1:n.498C>T
ENST00000693560.1:c.1096C>T
ENST00000371953.8:c.577C>T
ENST00000371953.7:c.577C>T
ENST00000472832.2:n.4C>T
NM_000314.5:c.577C>T
NM_000314.6:c.577C>T
NM_001304717.2:c.1096C>T
NM_001304718.1:c.-15C>T
NM_000314.7:c.577C>T
NM_001304717.5:c.1096C>T
NM_001304718.2:c.-15C>T
More

Likely Benign

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Conflicting Evidence"
Met criteria codes 3
PM2 BP4 BP7

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.577C>T (p.Leu193=) 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). PM2: Present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort. (PMID 27535533). BP4: Synonymous variant where at least 2 out of 3 in silico models predict no splicing impact. BP7: Variant is synonymous (silent) and no splicing impact is predicted.
Met criteria codes
PM2
0.0004% in gnomAD (1/251078); 0.0029% for Latino (AMR) (1/34566)
BP4
In silico splicing models predict no impact on splicing: NNSPLICE: no alternate donor or acceptor sites predicted, native acceptor (0.91) and native donor (0.98) predicted. MaxEnt: no alternate donor or acceptor sites predicted. Native donor (9.07).
BP7
Synonymous variant
Curation History
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