NM_000314.6(PTEN):c.-953C>G AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Apr 1, 2024
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:: RCV000590579.12

Allele description [Variation Report for NM_000314.6(PTEN):c.-953C>G]

NM_000314.6(PTEN):c.-953C>G

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.-953C>G

HGVS:

NC_000010.11:g.87863516C>G
NG_007466.2:g.5079C>G
NG_033079.1:g.4922G>C
NG_183718.1:g.237C>G
NM_000314.4:c.-953C>G
NM_000314.6:c.-953C>G
NM_001126049.2:c.-1029G>CMANE SELECT
NM_001304717.4:c.-434C>G
NM_001304718.1:c.-1658C>G
LRG_1087t1:c.-1029G>C
LRG_311t1:c.-953C>G
LRG_1087:g.4922G>C
LRG_311:g.5079C>G
NC_000010.10:g.89623273C>G

Links:

dbSNP: rs1465513356

NCBI 1000 Genomes Browser:

rs1465513356

Molecular consequence:

NM_001126049.2:c.-1029G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000680847	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Apr 1, 2024)	germline	clinical testing	Citation Link,
SCV000696553	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Aug 22, 2017)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000680847

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Apr 1, 2024)

germline

clinical testing

Citation Link,

SCV000696553

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Aug 22, 2017)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000680847.4

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

Description

Has not been previously published as pathogenic or benign to our knowledge

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696553.1

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

Description

Variant summary: The PTEN variant c.-953C>G (also known as c.-954C>G) involves the alteration of a non-conserved nucleotide. One in silico tool predicts a damaging outcome for this variant. This variant was found in 2/30866 control chromosomes in genomAD at a frequency of 0.0000648, which is approximately 10 times the estimated maximal expected allele frequency of a pathogenic PTEN variant (0.0000063), suggesting this variant is likely a benign polymorphism. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as a "Variant of Uncertain Significance - Possibly Benign."

#	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: Nov 3, 2024

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