NM_000249.4(MLH1):c.589-15C>T AND Colorectal cancer, hereditary nonpolyposis, type 2

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:: RCV001145067.6

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:: Colorectal cancer, hereditary nonpolyposis, type 2 (LYNCH2)
Synonyms:: COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 2; Lynch syndrome II; MLH1-Related Lynch Syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012249; MedGen: C1333991; Orphanet: 144; OMIM: 609310

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001305702	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV004015873	KCCC/NGS Laboratory, Kuwait Cancer Control Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jul 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001305702

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Jan 13, 2018)

germline

clinical testing

Citation Link,

SCV004015873

KCCC/NGS Laboratory, Kuwait Cancer Control Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jul 7, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical 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 Illumina Laboratory Services, Illumina, SCV001305702.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004015873.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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