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NM_000251.3(MSH2):c.1899A>T (p.Ile633=) AND Lynch syndrome 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 5, 2021
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:
RCV001310074.2

Allele description [Variation Report for NM_000251.3(MSH2):c.1899A>T (p.Ile633=)]

NM_000251.3(MSH2):c.1899A>T (p.Ile633=)

Gene:
MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_000251.3(MSH2):c.1899A>T (p.Ile633=)
HGVS:
  • NC_000002.12:g.47475164A>T
  • NG_007110.2:g.77041A>T
  • NM_000251.3:c.1899A>TMANE SELECT
  • NM_001258281.1:c.1701A>T
  • NP_000242.1:p.Ile633=
  • NP_001245210.1:p.Ile567=
  • LRG_218:g.77041A>T
  • NC_000002.11:g.47702303A>T
  • NM_000251.1:c.1899A>T
Links:
dbSNP: rs1667243318
NCBI 1000 Genomes Browser:
rs1667243318
Molecular consequence:
  • NM_000251.3:c.1899A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001258281.1:c.1701A>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Lynch syndrome 1
Synonyms:
COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 1; MSH2-Related Hereditary Non-Polyposis Colon Cancer; Lynch syndrome I; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007356; MedGen: C2936783; Orphanet: 144; OMIM: 120435

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001486201Institute of Human Genetics, University of Goettingen
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 5, 2021) 		germlineclinical 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

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 Institute of Human Genetics, University of Goettingen, SCV001486201.1

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

Description

This variant was not found in gnomAD and it is not described in the literature. This variant was found in a patient with CRC without microsatellite instability or loss of MMR protein expression hinting to a likely benign nature of the variant. The variant is neither predicted to be deleterious nor affecting splicing. In summary and using ACMG criteria PM2 the variant is classified as variant of unknown significance.

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

Last Updated: Sep 29, 2024