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

Germline classification:
Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:
Dec 1, 2022
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:
RCV000588071.33

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]
Observations:
3

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000225529Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)		Uncertain significance
(Feb 18, 2015) 		germlineclinical testing

Citation Link,

SCV000806198PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Sep 25, 2017) 		germlineclinical testing

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

SCV001747498CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)		Likely benign
(Dec 1, 2022) 		germlineclinical testing

Citation Link,

SCV001870716GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Benign
(Mar 3, 2015) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical testing
not providedgermlineyes2not providednot providednot providednot providedclinical 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 Eurofins Ntd Llc (ga), SCV000225529.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From PreventionGenetics, part of Exact Sciences, SCV000806198.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV001747498.20

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided

Description

PMS2: BP4, BP7

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From GeneDx, SCV001870716.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024