NM_000535.7(PMS2):c.353+9A>C AND not provided

Germline classification:: Benign (1 submission)
Last evaluated:: Aug 16, 2017
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:: RCV000588382.4

Allele description [Variation Report for NM_000535.7(PMS2):c.353+9A>C]

NM_000535.7(PMS2):c.353+9A>C

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.353+9A>C

HGVS:

NC_000007.14:g.6003681T>G
NG_008466.1:g.10426A>C
NM_000535.7:c.353+9A>CMANE SELECT
NM_001322003.2:c.-53+9A>C
NM_001322004.2:c.-53+9A>C
NM_001322005.2:c.-53+9A>C
NM_001322006.2:c.353+9A>C
NM_001322007.2:c.35+291A>C
NM_001322008.2:c.35+291A>C
NM_001322009.2:c.-53+9A>C
NM_001322010.2:c.-53+9A>C
NM_001322011.2:c.-532+9A>C
NM_001322012.2:c.-532+9A>C
NM_001322013.2:c.-53+9A>C
NM_001322014.2:c.353+9A>C
NM_001322015.2:c.-132+9A>C
LRG_161t1:c.353+9A>C
LRG_161:g.10426A>C
NC_000007.13:g.6043312T>G
NM_000535.5:c.353+9A>C
NM_000535.6:c.353+9A>C

Links:

dbSNP: rs139990791

NCBI 1000 Genomes Browser:

rs139990791

Molecular consequence:

NM_000535.7:c.353+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322003.2:c.-53+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322004.2:c.-53+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322005.2:c.-53+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322006.2:c.353+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322007.2:c.35+291A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.35+291A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322009.2:c.-53+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-53+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322011.2:c.-532+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322012.2:c.-532+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322013.2:c.-53+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322014.2:c.353+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322015.2:c.-132+9A>C - intron variant - [Sequence Ontology: SO:0001627]

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
SCV000697362	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Aug 16, 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

SCV000697362

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Aug 16, 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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697362.1

#	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 PMS2 c.353+9A>C variant involves the alteration of a non-conserved intronic nucleotideand 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 70/260874 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.002958 (67/22652). This frequency is about 26 times the estimated maximal expected allele frequency of a pathogenic PMS2 variant (0.0001136), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories classified this variant as "likely benign/benign." The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Taken together, this variant is classified as benign.

#	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: Sep 29, 2024

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