NM_000535.7(PMS2):c.1144+5G>C AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Dec 8, 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:
RCV001657463.4

Allele description [Variation Report for NM_000535.7(PMS2):c.1144+5G>C]

NM_000535.7(PMS2):c.1144+5G>C

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.1144+5G>C
HGVS:
  • NC_000007.14:g.5989795C>G
  • NG_008466.1:g.24312G>C
  • NM_000535.6:c.1144+5G>C
  • NM_000535.7:c.1144+5G>CMANE SELECT
  • NM_001322003.2:c.739+5G>C
  • NM_001322004.2:c.739+5G>C
  • NM_001322005.2:c.739+5G>C
  • NM_001322006.2:c.989-2175G>C
  • NM_001322007.2:c.826+5G>C
  • NM_001322008.2:c.826+5G>C
  • NM_001322009.2:c.739+5G>C
  • NM_001322010.2:c.584-2175G>C
  • NM_001322011.2:c.211+5G>C
  • NM_001322012.2:c.211+5G>C
  • NM_001322013.2:c.571+5G>C
  • NM_001322014.2:c.1144+5G>C
  • NM_001322015.2:c.835+5G>C
  • LRG_161:g.24312G>C
  • NC_000007.13:g.6029426C>G
Links:
dbSNP: rs1783506726
NCBI 1000 Genomes Browser:
rs1783506726
Molecular consequence:
  • NM_000535.7:c.1144+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322003.2:c.739+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322004.2:c.739+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322005.2:c.739+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322006.2:c.989-2175G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322007.2:c.826+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322008.2:c.826+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322009.2:c.739+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322010.2:c.584-2175G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322011.2:c.211+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322012.2:c.211+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322013.2:c.571+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322014.2:c.1144+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322015.2:c.835+5G>C - intron variant - [Sequence Ontology: SO:0001627]

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
SCV001870166GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely benign
(Feb 15, 2019) 		germlineclinical testing

Citation Link,

SCV004218939Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)		Uncertain significance
(Dec 8, 2022) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From GeneDx, SCV001870166.1

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004218939.1

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

Description

To the best of our knowledge, the variant has not been reported in the published literature. It also has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper PMS2 mRNA splicing . Based on the available information, we are unable to determine the clinical significance of this variant.

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

Last Updated: Feb 20, 2024