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.-1142C>T

CA151480

127661 (ClinVar)

Gene: KLLN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: b49fa554-1a60-419c-8931-6cdc5564285c

Approved on: 2018-04-06

Published on: 2018-12-10

HGVS expressions

NM_000314.6:c.-1142C>T

NM_000314.6(PTEN):c.-1142C>T

NM_001126049.1:c.-840G>A

ENST00000371953.7:c.-1143C>T

ENST00000445946.3:c.-840G>A

NC_000010.11:g.87863327C>T

CM000672.2:g.87863327C>T

NC_000010.10:g.89623084C>T

CM000672.1:g.89623084C>T

NC_000010.9:g.89613064C>T

NG_007466.2:g.4890C>T

NG_033079.1:g.5111G>A

Likely Benign

BS1 BP2

Evidence Links 0

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

PTEN c.-1142C>T (NC_000010.10:g.89623084C>T) meets criteria to be classified as likely 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). BS1: Allele frequency of 0.0049 (0.49%, 8/1622 alleles) in the East Asian subpopulation of the gnomAD cohort. (PMID 27535533) BP2: Observed in trans with a pathogenic or likely pathogenic PTEN variant, at least three observations in cis and/or phase unknown with different pathogenic/likely pathogenic PTEN variants. (Internal laboratory contributors SCV000187279.1, SCV000149465.6)

BS1

Allele frequency 0.0049 (8/1622, 0.49%) in East Asian individuals in gnomAD.

BP2

Multiple co-occurrences with pathogenic/likely pathogenic PTEN variants. 1 confirmed in trans, 3 with phase unknown.

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