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NM_000535.7(PMS2):c.2007-2A>G AND Lynch syndrome 4

Germline classification:
Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:
Sep 21, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV002467458.4

Allele description [Variation Report for NM_000535.7(PMS2):c.2007-2A>G]

NM_000535.7(PMS2):c.2007-2A>G

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.2007-2A>G
HGVS:
  • NC_000007.14:g.5982993T>C
  • NG_008466.1:g.31114A>G
  • NM_000535.7:c.2007-2A>GMANE SELECT
  • NM_001322003.2:c.1602-2A>G
  • NM_001322004.2:c.1602-2A>G
  • NM_001322005.2:c.1602-2A>G
  • NM_001322006.2:c.1851-2A>G
  • NM_001322007.2:c.1689-2A>G
  • NM_001322008.2:c.1689-2A>G
  • NM_001322009.2:c.1602-2A>G
  • NM_001322010.2:c.1446-2A>G
  • NM_001322011.2:c.1074-2A>G
  • NM_001322012.2:c.1074-2A>G
  • NM_001322013.2:c.1434-2A>G
  • NM_001322014.2:c.2007-2A>G
  • NM_001322015.2:c.1698-2A>G
  • NM_001406866.1:c.2193-2A>G
  • NM_001406868.1:c.2031-2A>G
  • NM_001406869.1:c.1899-2A>G
  • NM_001406870.1:c.1851-2A>G
  • NM_001406871.1:c.2007-2A>G
  • NM_001406872.1:c.2006+3766A>G
  • NM_001406873.1:c.1809-2A>G
  • NM_001406874.1:c.1839-2A>G
  • NM_001406875.1:c.1698-2A>G
  • NM_001406876.1:c.1689-2A>G
  • NM_001406877.1:c.1698-2A>G
  • NM_001406878.1:c.1698-2A>G
  • NM_001406879.1:c.1698-2A>G
  • NM_001406880.1:c.1698-2A>G
  • NM_001406881.1:c.1698-2A>G
  • NM_001406882.1:c.1698-2A>G
  • NM_001406883.1:c.1689-2A>G
  • NM_001406884.1:c.1683-2A>G
  • NM_001406885.1:c.1671-2A>G
  • NM_001406886.1:c.1641-2A>G
  • NM_001406887.1:c.1602-2A>G
  • NM_001406888.1:c.1602-2A>G
  • NM_001406889.1:c.1602-2A>G
  • NM_001406890.1:c.1602-2A>G
  • NM_001406891.1:c.1602-2A>G
  • NM_001406892.1:c.1602-2A>G
  • NM_001406893.1:c.1602-2A>G
  • NM_001406894.1:c.1602-2A>G
  • NM_001406895.1:c.1602-2A>G
  • NM_001406896.1:c.1602-2A>G
  • NM_001406897.1:c.1602-2A>G
  • NM_001406898.1:c.1602-2A>G
  • NM_001406899.1:c.1602-2A>G
  • NM_001406900.1:c.1542-2A>G
  • NM_001406901.1:c.1533-2A>G
  • NM_001406902.1:c.1533-2A>G
  • NM_001406903.1:c.1688+3766A>G
  • NM_001406904.1:c.1494-2A>G
  • NM_001406905.1:c.1494-2A>G
  • NM_001406906.1:c.1446-2A>G
  • NM_001406907.1:c.1446-2A>G
  • NM_001406908.1:c.1601+3766A>G
  • NM_001406909.1:c.1434-2A>G
  • NM_001406910.1:c.1601+3766A>G
  • NM_001406911.1:c.1236-2A>G
  • NM_001406912.1:c.804-2A>G
  • LRG_161t1:c.2007-2A>G
  • LRG_161:g.31114A>G
  • NC_000007.13:g.6022624T>C
  • NM_000535.5:c.2007-2A>G
  • NM_000535.7:c.2007-2A>G
Links:
dbSNP: rs587782336
NCBI 1000 Genomes Browser:
rs587782336
Molecular consequence:
  • NM_001406872.1:c.2006+3766A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406903.1:c.1688+3766A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406908.1:c.1601+3766A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406910.1:c.1601+3766A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000535.7:c.2007-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322003.2:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322004.2:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322005.2:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322006.2:c.1851-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322007.2:c.1689-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322008.2:c.1689-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322009.2:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322010.2:c.1446-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322011.2:c.1074-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322012.2:c.1074-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322013.2:c.1434-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322014.2:c.2007-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322015.2:c.1698-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406866.1:c.2193-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406868.1:c.2031-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406869.1:c.1899-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406870.1:c.1851-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406871.1:c.2007-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406873.1:c.1809-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406874.1:c.1839-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406875.1:c.1698-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406876.1:c.1689-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406877.1:c.1698-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406878.1:c.1698-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406879.1:c.1698-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406880.1:c.1698-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406881.1:c.1698-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406882.1:c.1698-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406883.1:c.1689-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406884.1:c.1683-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406885.1:c.1671-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406886.1:c.1641-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406887.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406888.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406889.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406890.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406891.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406892.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406893.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406894.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406895.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406896.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406897.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406898.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406899.1:c.1602-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406900.1:c.1542-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406901.1:c.1533-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406902.1:c.1533-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406904.1:c.1494-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406905.1:c.1494-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406906.1:c.1446-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406907.1:c.1446-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406909.1:c.1434-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406911.1:c.1236-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406912.1:c.804-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Lynch syndrome 4 (LYNCH4)
Synonyms:
Colorectal cancer, hereditary nonpolyposis, type 4; Hereditary non-polyposis colorectal cancer, type 4
Identifiers:
MONDO: MONDO:0013699; MedGen: C1838333; Orphanet: 144; OMIM: 614337

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002762838Centre for Mendelian Genomics, University Medical Centre Ljubljana
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Dec 9, 2022) 		germlineresearch

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

SCV004187633Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))		Likely pathogenic
(Sep 21, 2023) 		unknownclinical testing

Citation Link,

SCV004207860Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Mar 31, 2023) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedresearch
not providedunknownunknownnot providednot 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 Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV002762838.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)

Description

PVS1_STR, PS4_STR, PM2_SUP

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

From Myriad Genetics, Inc., SCV004187633.1

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

Description

This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.

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

From Baylor Genetics, SCV004207860.1

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

Last Updated: Sep 29, 2024