NM_000314.8(PTEN):c.-802G>A AND PTEN hamartoma tumor syndrome

Germline classification:: Uncertain significance (2 submissions)
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:: RCV000988410.4

Allele description [Variation Report for NM_000314.8(PTEN):c.-802G>A]

NM_000314.8(PTEN):c.-802G>A

Genes:

LOC130004273:ATAC-STARR-seq lymphoblastoid silent region 2585 [Gene]
PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_000314.8(PTEN):c.-802G>A

Other names:

NM_000314.7(PTEN):c.-801G>A; c.-802G>A

HGVS:

NC_000010.11:g.87863668G>A
NG_007466.2:g.5231G>A
NG_033079.1:g.4770C>T
NM_000314.8:c.-802G>AMANE SELECT
NM_001304717.5:c.-282G>A
NM_001304718.2:c.-1506G>A
LRG_311t1:c.-801G>A
LRG_1087:g.4770C>T
LRG_311:g.5231G>A
NC_000010.10:g.89623425G>A
NM_000314.4:c.-801G>A

Links:

dbSNP: rs876661166

NCBI 1000 Genomes Browser:

rs876661166

Molecular consequence:

NM_000314.8:c.-802G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001304717.5:c.-282G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001304718.2:c.-1506G>A - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001138119	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Likely benign (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV002576574	Clingen PTEN Variant Curation Expert Panel, Clingen	reviewed by expert panel (ClinGen PTEN ACMG Specifications v2)	Uncertain significance (Oct 20, 2020)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001138119

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Likely benign
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV002576574

Clingen PTEN Variant Curation Expert Panel, Clingen

reviewed by expert panel

(ClinGen PTEN ACMG Specifications v2)

Uncertain significance
(Oct 20, 2020)

germline

curation

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Mendelics, SCV001138119.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clingen PTEN Variant Curation Expert Panel, Clingen, SCV002576574.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not provided

Description

PTEN c.-802G>A, also described as c.-801G>A (NC_000010.11:g.87863668G>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). PM2: Absent in large sequenced populations

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 23, 2024

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