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]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_000314.8(PTEN):c.651C>T (p.Val217=)

CA10587096

255814 (ClinVar)

Gene: PTEN (HGNC:5728)
Condition: PTEN hamartoma tumor syndrome (MONDO:0017623)
Inheritance Mode: Autosomal dominant inheritance
UUID: 2f3d636c-4b73-48ee-93dd-243ce38e9778
Approved on: 2018-07-25
Published on: 2018-12-10

HGVS expressions

NM_000314.8(PTEN):c.651C>T (p.Val217=)
NM_000314.8:c.651C>T
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
ENST00000700029.2:c.651C>T
ENST00000710265.1:c.651C>T
ENST00000472832.3:c.651C>T
ENST00000688158.2:n.1386C>T
ENST00000688922.2:c.*481C>T
ENST00000700021.1:c.606C>T
ENST00000700022.1:c.509C>T
ENST00000700023.1:n.1809C>T
ENST00000700024.1:n.2043C>T
ENST00000700025.1:n.1420C>T
ENST00000700026.1:n.288C>T
ENST00000700029.1:c.485C>T
ENST00000706954.1:c.651C>T
ENST00000706955.1:c.*686C>T
ENST00000686459.1:c.*237C>T
ENST00000688158.1:c.*762C>T
ENST00000688308.1:c.651C>T
ENST00000688922.1:c.572C>T
ENST00000693560.1:c.1170C>T
ENST00000371953.8:c.651C>T
ENST00000371953.7:c.651C>T
ENST00000472832.2:c.78C>T
NM_000314.5:c.651C>T
NM_000314.6: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
More

Likely Benign

Met criteria codes 3
BP7 BP4 PM2_Supporting
Not Met criteria codes 23
PM3 PM1 PM4 PM5 PM6 BS2 BS4 BS3 BS1 PVS1 PS2 PS4 PS3 PS1 BP5 BP2 BP3 BP1 BA1 PP4 PP1 PP2 PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.2.0

Criteria Specification Approval History
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 (ACMG Classification Rules Specified for PTEN Variant Curation version 3.1.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PM2_Supporting: 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
BP7
SpliceAI predicts no impact on splicing (Scores are <0.2) nor the creation of a new splice site. The nucleotide is not highly conserved (PhyloP 0.377).
BP4
SpliceAI predicts no splicing impact​ (Scores <0.2 are considered evidence of benign.)
PM2_Supporting
Absent in gnomAD v2 and v4.
Not Met criteria codes
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
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
BS1
Absent gnomAD I agree (FH)
PVS1
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
PS4
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
PS1
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
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
BA1
Absent gnomAD I agree (FH)
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
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
Curation History
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