NM_000249.4(MLH1):c.885-21TC[2] AND Lynch syndrome II

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: May 28, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_000249.4(MLH1):c.885-21TC[2]]


MLH1:mutL homolog 1 [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
  • NC_000003.12:g.37020290_37020291CT[2]
  • NG_007109.2:g.31941_31942CT[2]
  • NM_000249.4:c.885-21TC[2]MANE SELECT
  • NM_001167617.2:c.591-21TC[2]
  • NM_001167618.2:c.162-21TC[2]
  • NM_001167619.2:c.162-21TC[2]
  • NM_001258271.1:c.885-21TC[2]
  • NM_001258273.1:c.162-21TC[2]
  • NM_001258274.2:c.162-21TC[2]
  • NM_001354615.1:c.162-21TC[2]
  • NM_001354616.1:c.162-21TC[2]
  • NM_001354617.1:c.162-21TC[2]
  • NM_001354618.1:c.162-21TC[2]
  • NM_001354619.1:c.162-21TC[2]
  • NM_001354620.1:c.591-21TC[2]
  • NM_001354621.1:c.-139-21TC[2]
  • NM_001354622.1:c.-139-21TC[2]
  • NM_001354623.1:c.-139-21TC[2]
  • NM_001354624.1:c.-36-5348TC[2]
  • NM_001354625.1:c.-36-5348TC[2]
  • NM_001354626.1:c.-36-5348TC[2]
  • NM_001354627.1:c.-36-5348TC[2]
  • NM_001354628.1:c.885-21TC[2]
  • NM_001354629.1:c.786-21TC[2]
  • NM_001354630.1:c.885-21TC[2]
  • LRG_216:g.31941_31942CT[2]
  • NC_000003.11:g.37061780_37061781delTC
  • NC_000003.11:g.37061781_37061782CT[2]
  • NC_000003.12:g.37020294_37020295delCT
  • NM_000249.3:c.885-16_885-15delCT
dbSNP: rs267607804
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000249.4:c.885-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167617.2:c.591-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167618.2:c.162-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167619.2:c.162-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258271.1:c.885-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258273.1:c.162-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258274.2:c.162-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354615.1:c.162-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354616.1:c.162-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354617.1:c.162-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354618.1:c.162-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354619.1:c.162-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354620.1:c.591-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354621.1:c.-139-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354622.1:c.-139-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354623.1:c.-139-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354624.1:c.-36-5348TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354625.1:c.-36-5348TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354626.1:c.-36-5348TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354627.1:c.-36-5348TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354628.1:c.885-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354629.1:c.786-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354630.1:c.885-21TC[2] - intron variant - [Sequence Ontology: SO:0001627]


Lynch syndrome II (HNPCC2)
COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 2; MLH1-Related Hereditary Non-Polyposis Colon Cancer; MLH1-Related Lynch Syndrome; See all synonyms [MedGen]
MONDO: MONDO:0012249; MedGen: C1333991; Orphanet: 144; OMIM: 609310

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000781753Center for Human Genetics, Inc,Center for Human Genetics, Inccriteria provided, single submitter
Uncertain significance
(Nov 1, 2016)
germlineclinical testing

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

SCV001136389Mendelicscriteria provided, single submitter
Likely benign
(May 28, 2019)
unknownclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing



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]

Details of each submission

From Center for Human Genetics, Inc,Center for Human Genetics, Inc, SCV000781753.1

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

From Mendelics, SCV001136389.1

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

Last Updated: Aug 21, 2021

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