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NM_000535.7(PMS2):c.255G>A (p.Leu85=) AND Endometrial carcinoma

Germline classification:
Likely benign (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001355358.5

Allele description [Variation Report for NM_000535.7(PMS2):c.255G>A (p.Leu85=)]

NM_000535.7(PMS2):c.255G>A (p.Leu85=)

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.255G>A (p.Leu85=)
Other names:
p.L85L:CTG>CTA
HGVS:
  • NC_000007.14:g.6003788C>T
  • NG_008466.1:g.10319G>A
  • NM_000535.7:c.255G>AMANE SELECT
  • NM_001322003.2:c.-151G>A
  • NM_001322004.2:c.-151G>A
  • NM_001322005.2:c.-151G>A
  • NM_001322006.2:c.255G>A
  • NM_001322007.2:c.35+184G>A
  • NM_001322008.2:c.35+184G>A
  • NM_001322009.2:c.-151G>A
  • NM_001322010.2:c.-151G>A
  • NM_001322011.2:c.-630G>A
  • NM_001322012.2:c.-630G>A
  • NM_001322013.2:c.-151G>A
  • NM_001322014.2:c.255G>A
  • NM_001322015.2:c.-230G>A
  • NP_000526.2:p.Leu85=
  • NP_001308935.1:p.Leu85=
  • NP_001308943.1:p.Leu85=
  • LRG_161t1:c.255G>A
  • LRG_161:g.10319G>A
  • NC_000007.13:g.6043419C>T
  • NM_000535.5:c.255G>A
  • NM_000535.6:c.255G>A
  • NM_000535.7:c.255G>A
  • NR_136154.1:n.342G>A
  • p.L85L
Links:
dbSNP: rs200491279
NCBI 1000 Genomes Browser:
rs200491279
Molecular consequence:
  • NM_001322003.2:c.-151G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322004.2:c.-151G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322005.2:c.-151G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322009.2:c.-151G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322010.2:c.-151G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322011.2:c.-630G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322012.2:c.-630G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322013.2:c.-151G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322015.2:c.-230G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322007.2:c.35+184G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322008.2:c.35+184G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NR_136154.1:n.342G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000535.7:c.255G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322006.2:c.255G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322014.2:c.255G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Name:
Endometrial carcinoma
Synonyms:
Endometrial carcinoma, somatic
Identifiers:
MONDO: MONDO:0002447; MedGen: C0476089; OMIM: 608089; Human Phenotype Ontology: HP:0012114

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001550228Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Likely benignunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001550228.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The PMS2 p.Leu85= variant was not identified in the literature nor was it identified in the Genesight-COGR, Cosmic, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, Mismatch Repair Genes Variant Database, and Insight Hereditary Tumors Database. The variant was identified in dbSNP (ID: rs200491279) “With Likely benign allele”, ClinVar (as benign by GeneDx, and likely benign by Ambry Genetics, Invitae and Color Genomics Inc.), Clinvitae (3x), and in control databases in 49 of 269350 chromosomes at a frequency of 0.0002 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017) being identified in the following populations: Other in 1 of 6368 chromosomes (frequency: 0.0002), Latino in 2 of 34332 chromosomes (frequency: 0.00006), European Non-Finnish in 45 of 123320 chromosomes (frequency: 0.0004) and in South Asian in 1 of 30744 chromosomes (frequency: 0.00003). The p.Leu85 variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 20, 2024