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NM_000249.4(MLH1):c.589-15C>T 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:
RCV000030229.6

Allele description [Variation Report for NM_000249.4(MLH1):c.589-15C>T]

NM_000249.4(MLH1):c.589-15C>T

Gene:
MLH1:mutL homolog 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p22.2
Genomic location:
Preferred name:
NM_000249.4(MLH1):c.589-15C>T
HGVS:
  • NC_000003.12:g.37011996C>T
  • NG_007109.2:g.23647C>T
  • NM_000249.4:c.589-15C>TMANE SELECT
  • NM_001167617.3:c.295-15C>T
  • NM_001167618.3:c.-135-15C>T
  • NM_001167619.3:c.-135-15C>T
  • NM_001258271.2:c.589-15C>T
  • NM_001258273.2:c.-135-15C>T
  • NM_001258274.3:c.-135-15C>T
  • NM_001354615.2:c.-135-15C>T
  • NM_001354616.2:c.-135-15C>T
  • NM_001354617.2:c.-135-15C>T
  • NM_001354618.2:c.-135-15C>T
  • NM_001354619.2:c.-135-15C>T
  • NM_001354620.2:c.295-15C>T
  • NM_001354621.2:c.-228-15C>T
  • NM_001354622.2:c.-341-15C>T
  • NM_001354623.2:c.-341-15C>T
  • NM_001354624.2:c.-238-15C>T
  • NM_001354625.2:c.-238-15C>T
  • NM_001354626.2:c.-238-15C>T
  • NM_001354627.2:c.-238-15C>T
  • NM_001354628.2:c.589-15C>T
  • NM_001354629.2:c.490-15C>T
  • NM_001354630.2:c.589-15C>T
  • LRG_216t1:c.589-15C>T
  • LRG_216:g.23647C>T
  • NC_000003.11:g.37053487C>T
  • NM_000249.3:c.589-15C>T
Links:
dbSNP: rs55658850
NCBI 1000 Genomes Browser:
rs55658850
Molecular consequence:
  • NM_000249.4:c.589-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167617.3:c.295-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167618.3:c.-135-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167619.3:c.-135-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258271.2:c.589-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258273.2:c.-135-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258274.3:c.-135-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354615.2:c.-135-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354616.2:c.-135-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354617.2:c.-135-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354618.2:c.-135-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354619.2:c.-135-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354620.2:c.295-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354621.2:c.-228-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354622.2:c.-341-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354623.2:c.-341-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354624.2:c.-238-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354625.2:c.-238-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354626.2:c.-238-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354627.2:c.-238-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354628.2:c.589-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354629.2:c.490-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354630.2:c.589-15C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

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

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000052896Women's Health and Genetics/Laboratory Corporation of America, LabCorp
no assertion criteria provided
Benign
(Apr 22, 2011) 		germlineclinical testing

SCV000106788International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
reviewed by expert panel

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

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, research

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000052896.2

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

From International Society for Gastrointestinal Hereditary Tumours (InSiGHT), SCV000106788.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided

Description

MAF >1% in African population

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

Last Updated: Sep 29, 2024