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NM_000314.6(PTEN):c.-909T>C AND PTEN hamartoma tumor syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jul 25, 2018
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000758225.9

Allele description [Variation Report for NM_000314.6(PTEN):c.-909T>C]

NM_000314.6(PTEN):c.-909T>C

Genes:
PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
LOC130004273:ATAC-STARR-seq lymphoblastoid silent region 2585 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
10q23.31
Genomic location:
Preferred name:
NM_000314.6(PTEN):c.-909T>C
HGVS:
  • NC_000010.11:g.87863560T>C
  • NG_007466.2:g.5123T>C
  • NG_033079.1:g.4878A>G
  • NG_183718.1:g.281T>C
  • NM_000314.6:c.-909T>C
  • NM_001304717.4:c.-390T>C
  • NM_001304718.1:c.-1614T>C
  • LRG_311t1:c.-909T>C
  • LRG_1087:g.4878A>G
  • LRG_311:g.5123T>C
  • NC_000010.10:g.89623317T>C
  • NM_000314.4:c.-909T>C
  • NM_000314.8:c.-910T>CMANE SELECT
  • c.-910T>C[hg19]
Links:
dbSNP: rs550385924
NCBI 1000 Genomes Browser:
rs550385924

Condition(s)

Name:
PTEN hamartoma tumor syndrome (PHTS)
Synonyms:
PTEN Hamartomatous Tumour Syndrome
Identifiers:
MONDO: MONDO:0017623; MeSH: D006223; MedGen: C1959582

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000886860Clingen PTEN Variant Curation Expert Panel, Clingen
reviewed by expert panel

(ClinGen PTEN ACMG Specifications v1)		Likely benign
(Jul 25, 2018) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From Clingen PTEN Variant Curation Expert Panel, Clingen, SCV000886860.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

PTEN c.-909T>C (NC_000010.10:g.87863560T>C) 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). BP2: Observed in trans with a pathogenic or likely pathogenic PTEN variant. (internal laboratory contributor ClinVar Organization ID 19864) BP5: Variant found in multiple cases with alternate molecular basis for disease. (internal laboratory contributors SCV000185347.1, SCV000149485.5)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 23, 2024