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]
Link to SEPIO compliant JSON-LD document

Variant: NM_000314.6(PTEN):c.79+7A>G

CA000580

127692 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 3acf8a70-e306-4b52-9401-648b6e0a3c99

HGVS expressions

NM_000314.6:c.79+7A>G
NM_000314.6(PTEN):c.79+7A>G
NC_000010.11:g.87864555A>G
CM000672.2:g.87864555A>G
NC_000010.10:g.89624312A>G
CM000672.1:g.89624312A>G
NC_000010.9:g.89614292A>G
NG_007466.2:g.6117A>G
NG_033079.1:g.3883T>C
ENST00000686459.1:c.79+7A>G
ENST00000688158.1:c.79+7A>G
ENST00000688308.1:c.79+7A>G
ENST00000693560.1:c.598+7A>G
ENST00000371953.8:c.79+7A>G
ENST00000371953.7:c.79+7A>G
ENST00000462694.1:n.81+7A>G
ENST00000487939.1:n.100+7A>G
ENST00000610634.1:c.-24+7A>G
ENST00000618586.1:n.55A>G
NM_000314.5:c.79+7A>G
NM_001304717.2:c.598+7A>G
NM_001304718.1:c.-627+7A>G
NM_000314.7:c.79+7A>G
NM_001304717.5:c.598+7A>G
NM_001304718.2:c.-627+7A>G
NM_000314.8:c.79+7A>G
NM_000314.8(PTEN):c.79+7A>G

Likely Benign

Met criteria codes 1
BS3
Not Met criteria codes 25
BS2 BS4 BS1 PVS1 BP5 BP7 BP2 BP3 BP1 BP4 PS4 PS2 PS3 PS1 BA1 PP1 PP4 PP2 PP3 PM6 PM2 PM3 PM1 PM4 PM5

Evidence Links 3

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
NM_000314.8(PTEN):c.79+7A>G variant 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 3.0.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). BS3: Intronic variant with RNA, mini-gene, or other splicing assay demonstrating no splicing impact. (PMID: 28677221)
Met criteria codes
BS3
Intronic variant with RNA, mini-gene, or other splicing assay demonstrating no splicing impact. (Chen HJ et al. 2017 PMID: 28677221 showed c.79+7A>G had no demonstrated splicing impact)
Variant reported to not demonstrate splicing impact, but results not shown. PubMed:28677221
Not Met criteria codes
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
BS1
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
BP5
2 internal GDx cases, but both with overlapping diagnoses with PHTS.
BP7
In silico predictors not able to detect native site.
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
BP4
Per Jessi: Near intron 1 splice donor, predictors can't detect native site. Would NOT apply PP3/BP4. Per Felicia, I agree PP3/BP4 would not apply.
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
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
BA1
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
Variant reported in two adults with CC scores of 11 and 2 respectively. No PP4 criteria met. PubMed:28677221
Reported in a pt with features of PHTS; no specifics provided. Would also be in Chen 2017 paper. Omit. PubMed:25669429
Identified in pt undergoing clinical PTEN testing; no phenotype info provided. Omit. PubMed:21659347
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
Per Jessi: Near intron 1 splice donor, predictors can't detect native site. Would NOT apply PP3/BP4. Per Felicia, I agree PP3/BP4 would not apply.
PM6
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
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
Approved on: 2023-06-14
Published on: 2023-10-19
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