NM_000535.7(PMS2):c.2346C>T (p.Asp782=) AND not specified

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Aug 29, 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:: RCV000437642.2

Allele description [Variation Report for NM_000535.7(PMS2):c.2346C>T (p.Asp782=)]

NM_000535.7(PMS2):c.2346C>T (p.Asp782=)

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.2346C>T (p.Asp782=)

HGVS:

NC_000007.14:g.5977687G>A
NG_008466.1:g.36420C>T
NM_000535.7:c.2346C>TMANE SELECT
NM_001322003.2:c.1941C>T
NM_001322004.2:c.1941C>T
NM_001322005.2:c.1941C>T
NM_001322006.2:c.2190C>T
NM_001322007.2:c.2028C>T
NM_001322008.2:c.2028C>T
NM_001322009.2:c.1974C>T
NM_001322010.2:c.1785C>T
NM_001322011.2:c.1413C>T
NM_001322012.2:c.1413C>T
NM_001322013.2:c.1773C>T
NM_001322014.2:c.2379C>T
NM_001322015.2:c.2037C>T
NP_000526.2:p.Asp782=
NP_001308932.1:p.Asp647=
NP_001308933.1:p.Asp647=
NP_001308934.1:p.Asp647=
NP_001308935.1:p.Asp730=
NP_001308936.1:p.Asp676=
NP_001308937.1:p.Asp676=
NP_001308938.1:p.Asp658=
NP_001308939.1:p.Asp595=
NP_001308940.1:p.Asp471=
NP_001308941.1:p.Asp471=
NP_001308942.1:p.Asp591=
NP_001308943.1:p.Asp793=
NP_001308944.1:p.Asp679=
LRG_161t1:c.2346C>T
LRG_161:g.36420C>T
NC_000007.13:g.6017318G>A
NM_000535.5:c.2346C>T
NR_136154.1:n.2390C>T

Links:

dbSNP: rs139031103

NCBI 1000 Genomes Browser:

rs139031103

Molecular consequence:

NR_136154.1:n.2390C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000535.7:c.2346C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322003.2:c.1941C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322004.2:c.1941C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322005.2:c.1941C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322006.2:c.2190C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322007.2:c.2028C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322008.2:c.2028C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322009.2:c.1974C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322010.2:c.1785C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322011.2:c.1413C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322012.2:c.1413C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322013.2:c.1773C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322014.2:c.2379C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322015.2:c.2037C>T - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000515317	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely benign (Jan 3, 2017)	germline	clinical testing	Citation Link,
SCV000697344	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Aug 29, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000515317

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely benign
(Jan 3, 2017)

germline

clinical testing

Citation Link,

SCV000697344

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(Aug 29, 2019)

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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000515317.4

#	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, SCV000697344.2

#	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	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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