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NC_000010.11:g.87863299C>A AND PTEN hamartoma tumor syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 20, 2020
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:
RCV002286569.9

Allele description [Variation Report for NC_000010.11:g.87863299C>A]

NC_000010.11:g.87863299C>A

Genes:
PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
KLLN:killin, p53 regulated DNA replication inhibitor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q23.31
Genomic location:
Preferred name:
NC_000010.11:g.87863299C>A
Other names:
NM_000314.7(PTEN):c.-1170C>A; NM_001126049.1(KLLN):c.-812G>T; c.-1171C>A
HGVS:
  • NC_000010.11:g.87863299C>A
  • NG_007466.2:g.4862C>A
  • NG_033079.1:g.5139G>T
  • NG_183718.1:g.20C>A
  • NM_001126049.2:c.-812G>TMANE SELECT
  • LRG_1087t1:c.-812G>T
  • LRG_311t1:c.-1170C>A
  • LRG_1087:g.5139G>T
  • LRG_311:g.4862C>A
  • NC_000010.10:g.89623056C>A
  • NM_000314.4:c.-1170C>A
  • c.-1171C>A[hg19]
Links:
Counsyl: 304319; dbSNP: rs587779981
NCBI 1000 Genomes Browser:
rs587779981
Molecular consequence:
  • NM_001126049.2:c.-812G>T - 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
SCV002576578Clingen PTEN Variant Curation Expert Panel, Clingen
reviewed by expert panel

(ClinGen PTEN ACMG Specifications v2)		Uncertain significance
(Oct 20, 2020) 		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, SCV002576578.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

PTEN c.-1170C>A, also described as c.-1171C>A (NC_000010.10:g.89623056C>A) is currently classified as a variant of uncertain significance 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). No criteria currently apply to this variant.

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

Last Updated: Nov 3, 2024