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NM_000535.7(PMS2):c.2445+3A>T AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 17, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002446829.2

Allele description [Variation Report for NM_000535.7(PMS2):c.2445+3A>T]

NM_000535.7(PMS2):c.2445+3A>T

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.2445+3A>T
HGVS:
  • NC_000007.14:g.5977585T>A
  • NG_008466.1:g.36522A>T
  • NM_000535.7:c.2445+3A>TMANE SELECT
  • NM_001322003.2:c.2040+3A>T
  • NM_001322004.2:c.2040+3A>T
  • NM_001322005.2:c.2040+3A>T
  • NM_001322006.2:c.2289+3A>T
  • NM_001322007.2:c.2127+3A>T
  • NM_001322008.2:c.2127+3A>T
  • NM_001322009.2:c.2073+3A>T
  • NM_001322010.2:c.1884+3A>T
  • NM_001322011.2:c.1512+3A>T
  • NM_001322012.2:c.1512+3A>T
  • NM_001322013.2:c.1872+3A>T
  • NM_001322014.2:c.2478+3A>T
  • NM_001322015.2:c.2136+3A>T
  • LRG_161t1:c.2445+3A>T
  • LRG_161:g.36522A>T
  • NC_000007.13:g.6017216T>A
  • NM_000535.5:c.2445+3A>T
Links:
dbSNP: rs765667554
NCBI 1000 Genomes Browser:
rs765667554
Molecular consequence:
  • NM_000535.7:c.2445+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322003.2:c.2040+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322004.2:c.2040+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322005.2:c.2040+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322006.2:c.2289+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322007.2:c.2127+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322008.2:c.2127+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322009.2:c.2073+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322010.2:c.1884+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322011.2:c.1512+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322012.2:c.1512+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322013.2:c.1872+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322014.2:c.2478+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322015.2:c.2136+3A>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002732707Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Feb 17, 2022) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV002732707.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.2445+3A>T intronic variant results from an A to T substitution 3 nucleotides after coding exon 14 in the PMS2 gene. This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024