U.S. flag

An official website of the United States government

NM_000249.4(MLH1):c.546-16T>A AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 15, 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:
RCV001934988.6

Allele description [Variation Report for NM_000249.4(MLH1):c.546-16T>A]

NM_000249.4(MLH1):c.546-16T>A

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.546-16T>A
HGVS:
  • NC_000003.12:g.37011804T>A
  • NG_007109.2:g.23455T>A
  • NM_000249.4:c.546-16T>AMANE SELECT
  • NM_001167617.3:c.252-16T>A
  • NM_001167618.3:c.-178-16T>A
  • NM_001167619.3:c.-178-16T>A
  • NM_001258271.2:c.546-16T>A
  • NM_001258273.2:c.-178-16T>A
  • NM_001258274.3:c.-178-16T>A
  • NM_001354615.2:c.-178-16T>A
  • NM_001354616.2:c.-178-16T>A
  • NM_001354617.2:c.-178-16T>A
  • NM_001354618.2:c.-178-16T>A
  • NM_001354619.2:c.-178-16T>A
  • NM_001354620.2:c.252-16T>A
  • NM_001354621.2:c.-271-16T>A
  • NM_001354622.2:c.-384-16T>A
  • NM_001354623.2:c.-384-16T>A
  • NM_001354624.2:c.-281-16T>A
  • NM_001354625.2:c.-281-16T>A
  • NM_001354626.2:c.-281-16T>A
  • NM_001354627.2:c.-281-16T>A
  • NM_001354628.2:c.546-16T>A
  • NM_001354629.2:c.447-16T>A
  • NM_001354630.2:c.546-16T>A
  • LRG_216:g.23455T>A
  • NC_000003.11:g.37053295T>A
Links:
dbSNP: rs2125805002
NCBI 1000 Genomes Browser:
rs2125805002
Molecular consequence:
  • NM_000249.4:c.546-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167617.3:c.252-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167618.3:c.-178-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167619.3:c.-178-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258271.2:c.546-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258273.2:c.-178-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258274.3:c.-178-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354615.2:c.-178-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354616.2:c.-178-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354617.2:c.-178-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354618.2:c.-178-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354619.2:c.-178-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354620.2:c.252-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354621.2:c.-271-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354622.2:c.-384-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354623.2:c.-384-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354624.2:c.-281-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354625.2:c.-281-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354626.2:c.-281-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354627.2:c.-281-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354628.2:c.546-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354629.2:c.447-16T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354630.2:c.546-16T>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Hereditary nonpolyposis colorectal neoplasms
Identifiers:
MeSH: D003123; MedGen: C0009405

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002168174Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 15, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002168174.3

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with MLH1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 6 of the MLH1 gene. It does not directly change the encoded amino acid sequence of the MLH1 protein.

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

Last Updated: Sep 29, 2024