NM_000535.7(PMS2):c.353+3G>A AND not specified

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Oct 8, 2018
Review status:: criteria provided, conflicting classifications

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:: RCV000425644.4

Allele description [Variation Report for NM_000535.7(PMS2):c.353+3G>A]

NM_000535.7(PMS2):c.353+3G>A

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+3G>A

HGVS:

NC_000007.14:g.6003687C>T
NG_008466.1:g.10420G>A
NM_000535.7:c.353+3G>AMANE SELECT
NM_001322003.2:c.-53+3G>A
NM_001322004.2:c.-53+3G>A
NM_001322005.2:c.-53+3G>A
NM_001322006.2:c.353+3G>A
NM_001322007.2:c.35+285G>A
NM_001322008.2:c.35+285G>A
NM_001322009.2:c.-53+3G>A
NM_001322010.2:c.-53+3G>A
NM_001322011.2:c.-532+3G>A
NM_001322012.2:c.-532+3G>A
NM_001322013.2:c.-53+3G>A
NM_001322014.2:c.353+3G>A
NM_001322015.2:c.-132+3G>A
LRG_161t1:c.353+3G>A
LRG_161:g.10420G>A
NC_000007.13:g.6043318C>T
NM_000535.5:c.353+3G>A

Links:

dbSNP: rs766373982

NCBI 1000 Genomes Browser:

rs766373982

Molecular consequence:

NM_000535.7:c.353+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322003.2:c.-53+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322004.2:c.-53+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322005.2:c.-53+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322006.2:c.353+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322007.2:c.35+285G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.35+285G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322009.2:c.-53+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-53+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322011.2:c.-532+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322012.2:c.-532+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322013.2:c.-53+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322014.2:c.353+3G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322015.2:c.-132+3G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000527261	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely benign (May 2, 2016)	germline	clinical testing	Citation Link,
SCV000918038	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Oct 8, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000527261

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely benign
(May 2, 2016)

germline

clinical testing

Citation Link,

SCV000918038

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Oct 8, 2018)

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	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

Details of each submission

From GeneDx, SCV000527261.4

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000918038.1

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

Description

Variant summary: PMS2 c.353+3G>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4.3e-06 in 230064 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.353+3G>A in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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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