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NM_000314.6(PTEN):c.-975G>C AND PTEN hamartoma tumor syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jun 25, 2019
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:
RCV000790889.10

Allele description [Variation Report for NM_000314.6(PTEN):c.-975G>C]

NM_000314.6(PTEN):c.-975G>C

Genes:
PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
LOC130004273:ATAC-STARR-seq lymphoblastoid silent region 2585 [Gene]
KLLN:killin, p53 regulated DNA replication inhibitor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q23.31
Genomic location:
Preferred name:
NM_000314.6(PTEN):c.-975G>C
HGVS:
  • NC_000010.11:g.87863494G>C
  • NG_007466.2:g.5057G>C
  • NG_033079.1:g.4944C>G
  • NG_183718.1:g.215G>C
  • NM_000314.4:c.-975G>C
  • NM_000314.6:c.-975G>C
  • NM_001126049.2:c.-1007C>GMANE SELECT
  • NM_001304717.4:c.-456G>C
  • NM_001304718.1:c.-1680G>C
  • LRG_1087t1:c.-1007C>G
  • LRG_311t1:c.-975G>C
  • LRG_1087:g.4944C>G
  • LRG_311:g.5057G>C
  • NC_000010.10:g.89623251G>C
  • c.-976G>C[hg19]
Links:
dbSNP: rs587780001
NCBI 1000 Genomes Browser:
rs587780001
Molecular consequence:
  • NM_001126049.2:c.-1007C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

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
SCV000930123Clingen PTEN Variant Curation Expert Panel, Clingen
reviewed by expert panel

(ClinGen PTEN ACMG Specifications v1)		Likely benign
(Jun 25, 2019) 		germlinecuration

PubMed (1)
[See all records that cite this PMID]

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Analysis of protein-coding genetic variation in 60,706 humans.

Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, Cooper DN, Deflaux N, DePristo M, et al.

Nature. 2016 Aug 18;536(7616):285-91. doi: 10.1038/nature19057.

PubMed [citation]
PMID:
27535533
PMCID:
PMC5018207

Details of each submission

From Clingen PTEN Variant Curation Expert Panel, Clingen, SCV000930123.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

PTEN c.-975G>C (g.89623251G>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). BS1: Allele frequency of 0.006 (0.6%, 21/3466 alleles) in the European (Finnish) subpopulation and 0.002 (0.2%, 30/14,976) in the European (Non-Finnish) subpopulation of the gnomAD cohort. (PMID 27535533) BP5: Variant found in multiple cases with alternate molecular basis for disease. (internal laboratory contributors SCV000187238.1, SCV000149489.5)

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

Last Updated: Nov 3, 2024