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_000314.6(PTEN):c.651C>T (p.Val217=)

CA10587096

255814 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 2f3d636c-4b73-48ee-93dd-243ce38e9778
Approved on: 2018-07-25
Published on: 2018-12-10

HGVS expressions

NM_000314.6:c.651C>T
NM_000314.6(PTEN):c.651C>T (p.Val217=)
NC_000010.11:g.87957869C>T
CM000672.2:g.87957869C>T
NC_000010.10:g.89717626C>T
CM000672.1:g.89717626C>T
NC_000010.9:g.89707606C>T
NG_007466.2:g.99431C>T
NM_000314.5:c.651C>T
NM_001304717.2:c.1170C>T
NM_001304718.1:c.60C>T
NM_000314.7:c.651C>T
NM_001304717.5:c.1170C>T
NM_001304718.2:c.60C>T
ENST00000371953.7:c.651C>T
ENST00000472832.2:n.78C>T
More

Likely Benign

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Conflicting Evidence"
Met criteria codes 3
PM2 BP7 BP4
Not Met criteria codes 20
PP3 PP2 PP1 PP4 PM6 PM5 PM4 PM1 PVS1 BA1 BS2 BS1 BS3 BS4 BP5 BP2 PS1 PS3 PS4 PS2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.651C>T (p.V217=) 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: Absent in large sequenced populations (PMID 27535533). BP4: Synonymous variant where at least 2 out of 3 in silico models predict no splicing impact. BP7: Variant is synonymous (silent), nucleotide is not conserved, and no splicing impact is predicted.
Met criteria codes
PM2
Absent gnomAD I agree (FH)
BP7
But concern re: conservation. I agree (FH)
BP4
HSF and NNsplice appear no impact; MaxEnt found slight weakening of splice acceptor (-13.71%). Would like to review with biocuration team. I agree. (FH)
Not Met criteria codes
PP3
HSF and NNsplice appear no impact; MaxEnt found slight weakening of splice acceptor (-13.71%). Would like to review with biocuration team. I agree. (FH)
PP2
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
PP4
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
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
Absent gnomAD I agree (FH)
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
Absent gnomAD I agree (FH)
BS3
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
BP2
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
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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
Curation History
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