Evidence Repository - Clinical Genome Resources

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.-1026C>A

CA000105

138836 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: b70739f7-4e4b-4678-8c1b-43aa0547db91

HGVS expressions

NM_000314.6:c.-1026C>A

NM_000314.6(PTEN):c.-1026C>A

NM_000314.5:c.-1026C>A

NM_001304717.2:c.-507C>A

NM_001304718.1:c.-1731C>A

ENST00000371953.7:c.-1027C>A

ENST00000610634.1:c.-1129C>A

NC_000010.11:g.87863443C>A

CM000672.2:g.87863443C>A

NC_000010.10:g.89623200C>A

CM000672.1:g.89623200C>A

NC_000010.9:g.89613180C>A

NG_007466.2:g.5006C>A

NG_033079.1:g.4995G>T

Likely Benign

BP5 BS2_Supporting BS1

Evidence Links 0

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

PTEN c.-1026C>A (NC_000010.10:g.89623200C>A) meets criteria to be classified as likely benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (Mester et al. 2018; manuscript in preparation). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). BS1: Allele frequency of 0.0056 (0.56%, 173/30,898 alleles) in the gnomAD cohort. (PMID 27535533) BS2_P: Meets criteria for BS2 (observed in the homozygous state in at least one healthy or PHTS-unaffected individual) but BS1 is also applied. (Internal laboratory contributor(s) SCV000171228.5) BP5: Variant found in multiple cases with alternate molecular basis for disease. (Internal laboratory contributor(s) SCV000171228.5)

BP5

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

BS2_Supporting

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

Approved on: 2016-11-09

Published on: 2018-12-10

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