NM_000535.7(PMS2):c.706-5_706-4del AND Lynch syndrome 4

Germline classification:: Benign (2 submissions)
Last evaluated:: Jun 8, 2016
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:: RCV000625387.12

Allele description [Variation Report for NM_000535.7(PMS2):c.706-5_706-4del]

NM_000535.7(PMS2):c.706-5_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.706-5_706-4del

HGVS:

NC_000007.13:g.6037058_6037059del
NC_000007.14:g.5997442_5997443del
NG_008466.1:g.16679_16680del
NM_000535.5:c.706-20_706-19delTT
NM_000535.7:c.706-5_706-4delMANE SELECT
NM_001322003.2:c.301-5_301-4del
NM_001322004.2:c.301-5_301-4del
NM_001322005.2:c.301-5_301-4del
NM_001322006.2:c.706-5_706-4del
NM_001322007.2:c.388-5_388-4del
NM_001322008.2:c.388-5_388-4del
NM_001322009.2:c.301-5_301-4del
NM_001322010.2:c.301-5_301-4del
NM_001322011.2:c.-228-5_-228-4del
NM_001322012.2:c.-228-5_-228-4del
NM_001322013.2:c.133-5_133-4del
NM_001322014.2:c.706-5_706-4del
NM_001322015.2:c.397-5_397-4del
LRG_161t1:c.706-5_706-4del
LRG_161:g.16679_16680del
NC_000007.13:g.6037058_6037059del
NC_000007.13:g.6037058_6037059delAA
NC_000007.13:g.6037073_6037074del
NM_000535.5:c.706-20_706-19delTT
NM_000535.5:c.706-5_706-4del
NM_000535.5:c.706-5_706-4delTT
NM_000535.6:c.706-5_706-4delTT
NM_000535.7:c.706-5_706-4del
NM_000535.7:c.706-5_706-4delTTMANE SELECT

Links:

dbSNP: rs60794673

NCBI 1000 Genomes Browser:

rs60794673

Molecular consequence:

NM_000535.7:c.706-5_706-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322003.2:c.301-5_301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322004.2:c.301-5_301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322005.2:c.301-5_301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322006.2:c.706-5_706-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322007.2:c.388-5_388-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.388-5_388-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322009.2:c.301-5_301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.301-5_301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322011.2:c.-228-5_-228-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322012.2:c.-228-5_-228-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322013.2:c.133-5_133-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322014.2:c.706-5_706-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322015.2:c.397-5_397-4del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Lynch syndrome 4 (LYNCH4)
Synonyms:: Colorectal cancer, hereditary nonpolyposis, type 4; Hereditary non-polyposis colorectal cancer, type 4
Identifiers:: MONDO: MONDO:0013699; MedGen: C1838333; Orphanet: 144; OMIM: 614337

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000745196	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Benign (Jun 8, 2016)	germline	clinical testing	Citation Link,
SCV000745848	Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus	no assertion criteria provided (ACGS Guidelines, 2013)	Benign (May 8, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000745196

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

criteria provided, single submitter

(ACGS Guidelines, 2013)

Benign
(Jun 8, 2016)

germline

clinical testing

Citation Link,

SCV000745848

Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus

no assertion criteria provided

(ACGS Guidelines, 2013)

Benign
(May 8, 2015)

germline

clinical testing

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

Details of each submission

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000745196.1

#	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	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV000745848.1

#	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	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 20, 2024

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