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_000314.6(PTEN):c.79+20C>G

CA000575

140807 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 58d4d344-a1e3-409c-b952-bcb231e15d01
Approved on: 2023-08-04
Published on: 2023-10-19

HGVS expressions

NM_000314.6:c.79+20C>G
NM_000314.6(PTEN):c.79+20C>G
NC_000010.11:g.87864568C>G
CM000672.2:g.87864568C>G
NC_000010.10:g.89624325C>G
CM000672.1:g.89624325C>G
NC_000010.9:g.89614305C>G
NG_007466.2:g.6130C>G
NG_033079.1:g.3870G>C
ENST00000686459.1:c.79+20C>G
ENST00000688158.1:c.79+20C>G
ENST00000688308.1:c.79+20C>G
ENST00000693560.1:c.598+20C>G
ENST00000371953.8:c.79+20C>G
ENST00000371953.7:c.79+20C>G
ENST00000462694.1:n.81+20C>G
ENST00000487939.1:n.100+20C>G
ENST00000610634.1:c.-24+20C>G
ENST00000618586.1:n.68C>G
NM_000314.5:c.79+20C>G
NM_001304717.2:c.598+20C>G
NM_001304718.1:c.-627+20C>G
NM_000314.7:c.79+20C>G
NM_001304717.5:c.598+20C>G
NM_001304718.2:c.-627+20C>G
NM_000314.8:c.79+20C>G
NM_000314.8(PTEN):c.79+20C>G
More

Uncertain Significance

Met criteria codes 2
BP7 PM2_Supporting
Not Met criteria codes 24
BA1 BS2 BS4 BS3 BS1 BP2 BP3 BP1 BP4 BP5 PVS1 PS2 PS4 PS3 PS1 PP4 PP1 PP2 PP3 PM3 PM1 PM4 PM5 PM6

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 3.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.79+20C>G (IVS1+20C>G) is currently classified as a variant of uncertain significance 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). PM2_Supporting: Absent in large sequenced populations (PMID 27535533). BP7: Variant is intronic and at or beyond +7/-21, nucleotide is not conserved, and no splicing impact is predicted.
Met criteria codes
BP7
Applied given no cryptic site predicted, nucleotide not conserved.
PM2_Supporting
Absent in large sequenced populations OR present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort. (PMID 27535533). PM2 drops to PM2_P with V3 rules.
Not Met criteria codes
BA1
Agree is met (JM)
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
Agree is met (JM)
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
Alteration is in intron 1. JM: agree can't use in silico predictors.
BP5
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
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
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
Alteration is in intron 1. JM: agree can't use in silico predictors.
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
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.