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

Germline classification:: Benign (5 submissions)
Last evaluated:: May 28, 2019
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:: RCV000415703.8

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 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
SCV000493782	Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen	no assertion criteria provided (ACMG Guidelines, 2015)	Uncertain significance (Oct 23, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000734566	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Benign	germline	clinical testing
SCV000745197	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 28, 2017)	germline	clinical testing	Citation Link,
SCV000745847	Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus	no assertion criteria provided (ACGS Guidelines, 2013)	Likely benign (Apr 22, 2015)	germline	clinical testing	Citation Link,
SCV001137318	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Benign (May 28, 2019)	unknown	clinical testing	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
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen, SCV000493782.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000734566.1

#	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 Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000745197.1

#	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, SCV000745847.1

#	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 Mendelics, SCV001137318.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 29, 2024

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