NM_000314.6(PTEN):c.-903_-882dup AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 26, 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:: RCV000169829.19

Allele description [Variation Report for NM_000314.6(PTEN):c.-903_-882dup]

NM_000314.6(PTEN):c.-903_-882dup

Genes:

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

Variant type:

Duplication

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_000314.6(PTEN):c.-903_-882dup

HGVS:

NC_000010.11:g.87863566_87863587dup
NG_007466.2:g.5129_5150dup
NG_033079.1:g.4854_4875dup
NG_183718.1:g.287_308dup
NM_000314.4:c.-903_-882dup
NM_000314.6:c.-903_-882dup
NM_001304717.4:c.-384_-363dup
NM_001304718.1:c.-1608_-1587dup
LRG_311t1:c.-903_-882dup
LRG_1087:g.4854_4875dup
LRG_311:g.5129_5150dup
NC_000010.10:g.89623323_89623344dup
NM_000314.4:c.-903_-882dupGGGACTCTTTATGCGCTGCGGC
NM_000314.4:c.-904_-883dup
NM_000314.4:c.-904_-883dup
NM_000314.6:c.-903_-882dup22
NM_000314.6:c.-904_-883dup22
NM_000314.6:c.-904_-883dup22
c.-904_-883dupGGGACTCTTTATGCGCTGCGGC[hg19]

Links:

dbSNP: rs786204888

NCBI 1000 Genomes Browser:

rs786204888

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
SCV000222150	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Sep 26, 2024)	germline	clinical testing	Citation Link,
SCV004219146	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Jul 27, 2023)	unknown	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

SCV000222150

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Sep 26, 2024)

germline

clinical testing

Citation Link,

SCV004219146

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Jul 27, 2023)

unknown

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	yes	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

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From GeneDx, SCV000222150.9

#	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; Also known as c.-903_-882dup; Located in a regulatory region; in the absence of functional studies, the actual effect of this sequence change is unknown

#	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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004219146.1

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

Description

This variant has not been reported in the published literature. The frequency of this variant in the general population, 0.000064 (2/31202 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Based on the available information, we are unable to determine the clinical significance of this variant.

#	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

Last Updated: Nov 3, 2024

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