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]

Variant: NM_000314.6(PTEN):c.165-13_165-10delGTTT

Curation History

CA059366

189425 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: a81bf7b8-305b-4704-bf65-95e6aa54b5ba

Approved on: 2016-12-14

Published on: 2018-12-10

HGVS expressions

NM_000314.6:c.165-13_165-10delGTTT

NM_000314.6(PTEN):c.165-13_165-10delGTTT

NC_000010.11:g.87925500_87925503del

CM000672.2:g.87925500_87925503del

NC_000010.10:g.89685257_89685260del

CM000672.1:g.89685257_89685260del

NC_000010.9:g.89675237_89675240del

NG_007466.2:g.67062_67065del

NM_000314.5:c.165-13_165-10del

NM_000314.6:c.165-13_165-10del

NM_001304717.2:c.684-13_684-10del

NM_001304718.1:c.-541-5546_-541-5543del

NM_000314.7:c.165-13_165-10del

NM_001304717.5:c.684-13_684-10del

NM_001304718.2:c.-541-5546_-541-5543del

ENST00000371953.7:c.165-13_165-10del

ENST00000610634.1:c.63-13_63-10del

Likely Benign

BS1 BP4

Evidence Links 0

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

PTEN c.165-13_165-10delGTTT (IVS2-13_IVS2-10delGTTT) 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 0.0049 (0.49%, 112/22,776 alleles) in the African subpopulation of the gnomAD cohort. (PMID 27535533) BP4: Intronic variant where at least 2 out of 3 in silico models predict no splicing impact.

BS1

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

Curation History

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