Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

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

Help
Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Nov 30, 2020)
Last evaluated:
Jul 7, 2020
Accession:
VCV000229653.4
Variation ID:
229653
Description:
1bp deletion
Help

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

Allele ID
233863
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
10q23.31
Genomic location
10: 87960877 (GRCh38) GRCh38 UCSC
10: 89720634 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.89720648del
NC_000010.11:g.87960891del
NM_000314.7:c.802-3del
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:87960876:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTT
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA336332
dbSNP: rs34003473
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Nov 19, 2016 RCV000507987.3
Benign 1 criteria provided, single submitter Aug 15, 2015 RCV000196322.2
Benign 1 criteria provided, single submitter Jul 7, 2020 RCV000214333.2
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PTEN Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh38
GRCh37
1948 2185

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Nov 19, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV000604974.1
Submitted: (Jun 30, 2017)
Evidence details
Benign
(May 23, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine
Accession: SCV000712182.2
Submitted: (Mar 21, 2019)
Evidence details
Comment:
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 … (more)
Benign
(Jul 07, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000272934.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Benign
(Aug 15, 2015)
criteria provided, single submitter
Method: clinical testing
PTEN hamartoma tumor syndrome
Allele origin: germline
Invitae
Accession: SCV000252697.3
Submitted: (Jan 06, 2016)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000692020.1
Submitted: (Oct 31, 2017)
Evidence details

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs34003473...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 19, 2021