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_000314.7(PTEN):c.159A>G (p.Val53=)

CA000127

184020 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 995c0e99-dc70-494f-bb25-ccabe14633fb

Approved on: 2024-02-09

Published on: 2024-03-04

HGVS expressions

NM_000314.7:c.159A>G

NM_000314.7(PTEN):c.159A>G (p.Val53=)

NC_000010.11:g.87894104A>G

CM000672.2:g.87894104A>G

NC_000010.10:g.89653861A>G

CM000672.1:g.89653861A>G

NC_000010.9:g.89643841A>G

NG_007466.2:g.35666A>G

ENST00000700029.2:c.159A>G

ENST00000710265.1:c.159A>G

ENST00000472832.3:c.159A>G

ENST00000688158.2:n.899+13666A>G

ENST00000688922.2:c.159A>G

ENST00000700021.1:c.159A>G

ENST00000700022.1:c.159A>G

ENST00000706954.1:c.159A>G

ENST00000706955.1:c.*194A>G

ENST00000686459.1:c.159A>G

ENST00000688158.1:c.*275+13666A>G

ENST00000688308.1:c.159A>G

ENST00000688922.1:c.28A>G

ENST00000693560.1:c.678A>G

ENST00000371953.8:c.159A>G

ENST00000371953.7:c.159A>G

ENST00000462694.1:n.161A>G

ENST00000610634.1:c.57A>G

NM_000314.5:c.159A>G

NM_000314.6:c.159A>G

NM_001304717.2:c.678A>G

NM_001304718.1:c.-547A>G

NM_001304717.5:c.678A>G

NM_001304718.2:c.-547A>G

NM_000314.8:c.159A>G

NM_000314.8(PTEN):c.159A>G (p.Val53=)

Likely Benign

BP4 BS1_Supporting

BS2 BS4 BS3 BP5 BP7 BP3 BP2 BP1 PVS1 PS4 PS2 PS1 PS3 PP4 PP1 PP3 PP2 BA1 PM5 PM1 PM4 PM3 PM6 PM2

Evidence Links 0

Expert Panel

PTEN VCEP

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.159A>G (p.Val53=) 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). BS1_P: To be applied for variants with filtering allele frequency of 0.0000043 up to 0.000043 (0.00043% up to 0.0043%) in gnomAD. Popmax FAF of this variant=0.00004593 (9 alleles v4 gnomAD). BP4: Synonymous variant where SpliceAI model predict no splicing impact (acceptor gain 0.08, donor gain 0.13).

BP4

Synonymous variant where SpliceAI model predict no splicing impact (acceptor gain 0.08, donor gain 0.13).

BS1_Supporting

To be applied for variants with filtering allele frequency of 0.0000043 up to 0.000043 (0.00043% up to 0.0043%) in gnomAD. Popmax FAF of this variant=0.00004593 (9 alleles v4 gnomAD).

BS2