NM_000535.7(PMS2):c.2127C>T (p.Phe709=) AND not specified

Germline classification:: Likely benign (3 submissions)
Last evaluated:: Feb 6, 2024
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:: RCV000855625.5

Allele description [Variation Report for NM_000535.7(PMS2):c.2127C>T (p.Phe709=)]

NM_000535.7(PMS2):c.2127C>T (p.Phe709=)

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.2127C>T (p.Phe709=)

HGVS:

NC_000007.14:g.5982871G>A
NG_008466.1:g.31236C>T
NM_000535.7:c.2127C>TMANE SELECT
NM_001322003.2:c.1722C>T
NM_001322004.2:c.1722C>T
NM_001322005.2:c.1722C>T
NM_001322006.2:c.1971C>T
NM_001322007.2:c.1809C>T
NM_001322008.2:c.1809C>T
NM_001322009.2:c.1722C>T
NM_001322010.2:c.1566C>T
NM_001322011.2:c.1194C>T
NM_001322012.2:c.1194C>T
NM_001322013.2:c.1554C>T
NM_001322014.2:c.2127C>T
NM_001322015.2:c.1818C>T
NP_000526.2:p.Phe709=
NP_001308932.1:p.Phe574=
NP_001308933.1:p.Phe574=
NP_001308934.1:p.Phe574=
NP_001308935.1:p.Phe657=
NP_001308936.1:p.Phe603=
NP_001308937.1:p.Phe603=
NP_001308938.1:p.Phe574=
NP_001308939.1:p.Phe522=
NP_001308940.1:p.Phe398=
NP_001308941.1:p.Phe398=
NP_001308942.1:p.Phe518=
NP_001308943.1:p.Phe709=
NP_001308944.1:p.Phe606=
LRG_161t1:c.2127C>T
LRG_161:g.31236C>T
NC_000007.13:g.6022502G>A
NM_000535.5:c.2127C>T
NM_000535.6:c.2127C>T
NR_136154.1:n.2214C>T

Links:

dbSNP: rs199943748

NCBI 1000 Genomes Browser:

rs199943748

Molecular consequence:

NR_136154.1:n.2214C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000535.7:c.2127C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322003.2:c.1722C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322004.2:c.1722C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322005.2:c.1722C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322006.2:c.1971C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322007.2:c.1809C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322008.2:c.1809C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322009.2:c.1722C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322010.2:c.1566C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322011.2:c.1194C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322012.2:c.1194C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322013.2:c.1554C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322014.2:c.2127C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322015.2:c.1818C>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
SCV000697330	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,
SCV003839885	Genetic Services Laboratory, University of Chicago	no assertion criteria provided	Likely benign (Jun 28, 2022)	germline	clinical testing
SCV004243279	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Feb 6, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000697330

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,

SCV003839885

Genetic Services Laboratory, University of Chicago

no assertion criteria provided

Likely benign
(Jun 28, 2022)

germline

clinical testing

SCV004243279

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Feb 6, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	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

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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697330.2

#	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

From Genetic Services Laboratory, University of Chicago, SCV003839885.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, SCV004243279.1

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

Last Updated: Oct 20, 2024

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