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.210-39A>G

CA059509

255812 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 4a5c2162-2e71-48bc-a4f1-036d0801c4d7
Approved on: 2020-06-18
Published on: 2020-06-18

HGVS expressions

NM_000314.7:c.210-39A>G
NM_000314.7(PTEN):c.210-39A>G
NM_000314.5:c.210-39A>G
NM_000314.6:c.210-39A>G
NM_001304717.2:c.729-39A>G
NM_001304718.1:c.-541-39A>G
NM_001304717.5:c.729-39A>G
NM_001304718.2:c.-541-39A>G
NM_000314.8:c.210-39A>G
ENST00000371953.7:c.210-39A>G
ENST00000498703.1:n.36-39A>G
ENST00000610634.1:c.108-39A>G
NC_000010.11:g.87931007A>G
CM000672.2:g.87931007A>G
NC_000010.10:g.89690764A>G
CM000672.1:g.89690764A>G
NC_000010.9:g.89680744A>G
NG_007466.2:g.72569A>G
More

Benign

Met criteria codes 2
BA1 BS3
Not Met criteria codes 20
PM5 PM4 PM1 PM2 PM6 PVS1 BS2 BS1 BS4 BP4 BP2 BP5 BP7 PS1 PS4 PS2 PS3 PP2 PP3 PP1

Evidence Links 4

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.210-39A>G (IVS3-39A>G) 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 0.01015 (1.01%, 252/24,818 alleles) in the European (Finnish) subpopulation of the gnomAD cohort. (PMID 27535533) BS3: Intronic variant with RNA, mini-gene, or other splicing assay demonstrating no splicing impact. (PMID 28677221)
Met criteria codes
BA1
gnomAD V3 Finnish >1%.
BS3
RNA for our variant showed no change (PMID 28677221).
Authors characterized PTEN mRNA processing, analyzed PTEN expression, and downstream readouts of P-AKT and P-ERK1/2. RNA for our variant showed no change. PubMed:28677221
Not Met criteria codes
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
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
PVS1
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
ESP: 0.07% EUR allele frequency
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
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
BP5
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
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
Patients with our variant, however CC scores too low.
PubMed:9425889
PubMed:30306255
PubMed:16773562
PubMed:28677221
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
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
Curation History
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