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NM_000535.7(PMS2):c.164-9_178delinsGATCC AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 25, 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:
RCV002391046.2

Allele description

NM_000535.7(PMS2):c.164-9_178delinsGATCC

Gene:
PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
7p22.1
Genomic location:
Preferred name:
NM_000535.7(PMS2):c.164-9_178delinsGATCC
HGVS:
  • NC_000007.14:g.6004044_6004067del24insGGATC
  • NC_000007.14:g.6004044_6004067delinsGGATC
  • NG_008466.1:g.10040_10063delinsGATCC
  • NM_000535.7:c.164-9_178delinsGATCCMANE SELECT
  • NM_001322003.2:c.-242-9_-228delinsGATCC
  • NM_001322004.2:c.-242-9_-228delinsGATCC
  • NM_001322005.2:c.-242-9_-228delinsGATCC
  • NM_001322006.2:c.164-9_178delinsGATCC
  • NM_001322007.2:c.-52-9_-38delinsGATCC
  • NM_001322008.2:c.-52-9_-38delinsGATCC
  • NM_001322009.2:c.-242-9_-228delinsGATCC
  • NM_001322010.2:c.-242-9_-228delinsGATCC
  • NM_001322011.2:c.-721-9_-707delinsGATCC
  • NM_001322012.2:c.-721-9_-707delinsGATCC
  • NM_001322013.2:c.-242-9_-228delinsGATCC
  • NM_001322014.2:c.164-9_178delinsGATCC
  • NM_001322015.2:c.-321-9_-307delinsGATCC
  • LRG_161t1:c.164-9_178del24insGATCC
  • LRG_161:g.10040_10063delinsGATCC
  • NC_000007.13:g.6043675_6043698delinsGGATC
  • NM_000535.5:c.164-9_178del24insGATCC
  • NM_000535.6:c.164-9_178delinsGATCC
Links:
dbSNP: rs1583410952
NCBI 1000 Genomes Browser:
rs1583410952
Molecular consequence:
  • NM_000535.7:c.164-9_178delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322003.2:c.-242-9_-228delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322004.2:c.-242-9_-228delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322005.2:c.-242-9_-228delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322006.2:c.164-9_178delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322007.2:c.-52-9_-38delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322008.2:c.-52-9_-38delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322009.2:c.-242-9_-228delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322010.2:c.-242-9_-228delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322011.2:c.-721-9_-707delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322012.2:c.-721-9_-707delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322013.2:c.-242-9_-228delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322014.2:c.164-9_178delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322015.2:c.-321-9_-307delinsGATCC - splice acceptor variant - [Sequence Ontology: SO:0001574]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002703453Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Oct 25, 2022) 		germlineclinical testing

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

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women.

Breast Cancer Association Consortium., Dorling L, Carvalho S, Allen J, González-Neira A, Luccarini C, Wahlström C, Pooley KA, Parsons MT, Fortuno C, Wang Q, Bolla MK, Dennis J, Keeman R, Alonso MR, Álvarez N, Herraez B, Fernandez V, Núñez-Torres R, Osorio A, Valcich J, Li M, et al.

N Engl J Med. 2021 Feb 4;384(5):428-439. doi: 10.1056/NEJMoa1913948. Epub 2021 Jan 20.

PubMed [citation]
PMID:
33471991
PMCID:
PMC7611105

Details of each submission

From Ambry Genetics, SCV002703453.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The c.164-9_178del24insGATCC variant spans the canonical acceptor site of coding exon 3 of the PMS2 gene. This variant results from a deletion of 24 nucleotides and insertion of GATCC nucleotides at positions c.164-9 to c.178. The canonical acceptor site is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and may result in the creation or strengthening of a novel splice acceptor site. 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: May 1, 2024