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NM_000179.3(MSH6):c.3557-40T>A AND Lynch syndrome 5

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Jul 7, 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:
RCV000986735.3

Allele description [Variation Report for NM_000179.3(MSH6):c.3557-40T>A]

NM_000179.3(MSH6):c.3557-40T>A

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.3557-40T>A
HGVS:
  • NC_000002.12:g.47805578T>A
  • NG_007111.1:g.27432T>A
  • NG_008397.1:g.105098A>T
  • NM_000179.3:c.3557-40T>AMANE SELECT
  • NM_001281492.2:c.3167-40T>A
  • NM_001281493.2:c.2651-40T>A
  • NM_001281494.2:c.2651-40T>A
  • LRG_219t1:c.3557-40T>A
  • LRG_219:g.27432T>A
  • NC_000002.11:g.48032717T>A
  • NM_000179.2:c.3557-40T>A
Links:
dbSNP: rs189436849
NCBI 1000 Genomes Browser:
rs189436849
Molecular consequence:
  • NM_000179.3:c.3557-40T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001281492.2:c.3167-40T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001281493.2:c.2651-40T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001281494.2:c.2651-40T>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Lynch syndrome 5 (LYNCH5)
Synonyms:
Colorectal cancer, hereditary nonpolyposis, type 5; Hereditary non-polyposis colorectal cancer, type 5
Identifiers:
MONDO: MONDO:0013710; MedGen: C1833477; Orphanet: 144; OMIM: 614350

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001135840Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)		Likely benign
(May 28, 2019) 		unknownclinical testing

Citation Link,

SCV004015984KCCC/NGS Laboratory, Kuwait Cancer Control Center
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Jul 7, 2023) 		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
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 Mendelics, SCV001135840.1

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

From KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004015984.1

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

Last Updated: Oct 8, 2024