NM_000535.7(PMS2):c.706-4del AND Lynch syndrome

Germline classification:: Benign (2 submissions)
Last evaluated:: Jul 10, 2015
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000203188.2

Allele description [Variation Report for NM_000535.7(PMS2):c.706-4del]

NM_000535.7(PMS2):c.706-4del

Gene:

PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.706-4del

HGVS:

NC_000007.13:g.6037058del
NC_000007.14:g.5997443del
NG_008466.1:g.16680del
NM_000535.7:c.706-4delMANE SELECT
NM_001322003.2:c.301-4del
NM_001322004.2:c.301-4del
NM_001322005.2:c.301-4del
NM_001322006.2:c.706-4del
NM_001322007.2:c.388-4del
NM_001322008.2:c.388-4del
NM_001322009.2:c.301-4del
NM_001322010.2:c.301-4del
NM_001322011.2:c.-228-4del
NM_001322012.2:c.-228-4del
NM_001322013.2:c.133-4del
NM_001322014.2:c.706-4del
NM_001322015.2:c.397-4del
LRG_161t1:c.706-4del
LRG_161:g.16680del
NC_000007.13:g.6037058del
NC_000007.13:g.6037058delA
NC_000007.13:g.6037074del
NM_000535.5:c.706-4del
NM_000535.5:c.706-4delT
NM_000535.5:c.706-5delT
NM_000535.6:c.706-4delT
NM_000535.6:c.706-5del
NM_000535.6:c.706-5delT
NM_000535.5:c.706-4delT

Links:

Ambry Genetics: a02961; dbSNP: rs60794673

NCBI 1000 Genomes Browser:

rs60794673

Molecular consequence:

NM_000535.7:c.706-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322003.2:c.301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322004.2:c.301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322005.2:c.301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322006.2:c.706-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322007.2:c.388-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.388-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322009.2:c.301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322011.2:c.-228-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322012.2:c.-228-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322013.2:c.133-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322014.2:c.706-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322015.2:c.397-4del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Lynch syndrome
Identifiers:: MONDO: MONDO:0005835; MedGen: C4552100

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000257705	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	criteria provided, single submitter (DGD Variant Analysis Guidelines)	Benign (Apr 17, 2015)	unknown	clinical testing	DGD_Variant_Analysis_Guidelines.docx, Citation Link,
SCV000257707	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	criteria provided, single submitter (DGD Variant Analysis Guidelines)	Benign (Jul 10, 2015)	unknown	clinical testing	DGD_Variant_Analysis_Guidelines.docx Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000257705

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

criteria provided, single submitter

(DGD Variant Analysis Guidelines)

Benign
(Apr 17, 2015)

unknown

clinical testing

DGD_Variant_Analysis_Guidelines.docx,

Citation Link,

SCV000257707

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

criteria provided, single submitter

(DGD Variant Analysis Guidelines)

Benign
(Jul 10, 2015)

unknown

clinical testing

DGD_Variant_Analysis_Guidelines.docx

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, SCV000257705.2

#	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 Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, SCV000257707.2

#	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

Last Updated: Sep 29, 2024

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