NM_000314.6(PTEN):c.-904C>A AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 27, 2023
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:: RCV000588831.16

Allele description [Variation Report for NM_000314.6(PTEN):c.-904C>A]

NM_000314.6(PTEN):c.-904C>A

Genes:

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

Variant type:

single nucleotide variant

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_000314.6(PTEN):c.-904C>A

HGVS:

NC_000010.11:g.87863565C>A
NG_007466.2:g.5128C>A
NG_033079.1:g.4873G>T
NG_183718.1:g.286C>A
NM_000314.4:c.-904C>A
NM_000314.6:c.-904C>A
NM_001304717.4:c.-385C>A
NM_001304718.1:c.-1609C>A
LRG_311t1:c.-904C>A
LRG_1087:g.4873G>T
LRG_311:g.5128C>A
NC_000010.10:g.89623322C>A
c.-905C>A[hg19]

Links:

dbSNP: rs587779997

NCBI 1000 Genomes Browser:

rs587779997

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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brain-derived neurotrophic factor, partial [Stigmochelys pardalis]
brain-derived neurotrophic factor, partial [Stigmochelys pardalis]
gi|374115370|gb|AEY99541.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000149483	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Dec 27, 2023)	germline	clinical testing	Citation Link,
SCV000696546	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (May 15, 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

SCV000149483

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Dec 27, 2023)

germline

clinical testing

Citation Link,

SCV000696546

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(May 15, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000149483.10

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

Description

No data available from control populations to assess the frequency of this variant; Has not been previously published as pathogenic or benign to our knowledge; Also known as c.-904C>A

#	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, SCV000696546.1

#	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 c.-904C>A (also known as c.-905C>A) variant involves the alteration of a non-conserved nucleotide located in the promoter region of PTEN. The variant of interest is absent in 30804 control chromosomes (gnomAD). In addition, a clinical diagnostic laboratory classified this variant as uncertain significance. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. Because of the absence of clinical information and the lack of functional studies, the variant is classified as a "Variant of Uncertain Significance (VUS)," until additional information becomes available.

#	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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