NM_000314.7(PTEN):c.802-3del AND not specified

This record was updated by the submitter. Please see the current version.

Germline classification:: Benign (3 submissions)
Last evaluated:: Nov 19, 2016
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000507987.3

Allele description

NM_000314.7(PTEN):c.802-3del

Gene:

PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_000314.7(PTEN):c.802-3del

HGVS:

NC_000010.11:g.87960891del
NG_007466.2:g.102453del
NM_000314.7:c.802-3del
NM_001304717.5:c.1322-3del
NM_001304718.2:c.211-3del
LRG_311t1:c.802-3del
LRG_311:g.102453del
NC_000010.10:g.89720648del
NM_000314.4:c.802-3delT
NM_000314.6:c.802-3del
NM_000314.6:c.802-3delT
NM_000314.4:c.802-3delT

Links:

dbSNP: rs34003473

NCBI 1000 Genomes Browser:

rs34003473

Molecular consequence:

NM_000314.7:c.802-3del - intron variant - [Sequence Ontology: SO:0001627]
NM_001304717.5:c.1322-3del - intron variant - [Sequence Ontology: SO:0001627]
NM_001304718.2:c.211-3del - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000604974	ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Benign (Nov 19, 2016)	germline	clinical testing	Citation Link,
SCV000692020	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Benign	unknown	clinical testing
SCV000712182	Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (May 23, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000604974

ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Benign
(Nov 19, 2016)

germline

clinical testing

Citation Link,

SCV000692020

Mayo Clinic Laboratories, Mayo Clinic

no assertion criteria provided

Benign

unknown

clinical testing

SCV000712182

Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(May 23, 2016)

germline

clinical testing

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

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	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories, SCV000604974.1

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV000692020.1

#	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 Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000712182.2

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

Description

c.802-3delT in intron 7 of PTEN: This variant is not expected to have clinical s ignificance because it has been identified in 33.66% (3462/10286) of South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitu te.org; dbSNP rs771859047).

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

Last Updated: Aug 14, 2021

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