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NM_000251.3(MSH2):c.6G>T (p.Ala2=) AND Lynch syndrome

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Sep 5, 2013
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV000076685.7

Allele description [Variation Report for NM_000251.3(MSH2):c.6G>T (p.Ala2=)]

NM_000251.3(MSH2):c.6G>T (p.Ala2=)

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.6G>T (p.Ala2=)
Other names:
p.A2A:GCG>GCT
HGVS:
  • NC_000002.12:g.47403197G>T
  • NG_007110.2:g.5074G>T
  • NM_000251.3:c.6G>TMANE SELECT
  • NM_001258281.1:c.-31+22G>T
  • NP_000242.1:p.Ala2=
  • NP_000242.1:p.Ala2=
  • LRG_218t1:c.6G>T
  • LRG_218:g.5074G>T
  • LRG_218p1:p.Ala2=
  • NC_000002.11:g.47630336G>T
  • NM_000251.1:c.6G>T
  • NM_000251.2:c.6G>T
  • p.A2A
Links:
dbSNP: rs368270856
NCBI 1000 Genomes Browser:
rs368270856
Molecular consequence:
  • NM_001258281.1:c.-31+22G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000251.3:c.6G>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
5

Condition(s)

Name:
Lynch syndrome
Identifiers:
MONDO: MONDO:0005835; MedGen: C4552100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000107720International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
reviewed by expert panel

(Guidelines v1.9)		Likely benign
(Sep 5, 2013) 		germlineresearch

Citation Link,

SCV004826183All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely Benign
(Feb 5, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown5not providednot provided108544not providedclinical testing, research

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 International Society for Gastrointestinal Hereditary Tumours (InSiGHT), SCV000107720.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided

Description

Multifactorial likelihood analysis posterior probability 0.001-0.049

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

From All of Us Research Program, National Institutes of Health, SCV004826183.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided5not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided5not providednot providednot provided

Last Updated: May 1, 2024