NM_000249.4(MLH1):c.1039-4A>G AND Colorectal cancer, hereditary nonpolyposis, type 2

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Mar 10, 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:: RCV000662614.2

Allele description [Variation Report for NM_000249.4(MLH1):c.1039-4A>G]

NM_000249.4(MLH1):c.1039-4A>G

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.1039-4A>G

HGVS:

NC_000003.12:g.37025633A>G
NG_007109.2:g.37284A>G
NM_000249.4:c.1039-4A>GMANE SELECT
NM_001167617.3:c.745-4A>G
NM_001167618.3:c.316-4A>G
NM_001167619.3:c.316-4A>G
NM_001258271.2:c.1039-4A>G
NM_001258273.2:c.316-4A>G
NM_001258274.3:c.316-4A>G
NM_001354615.2:c.316-4A>G
NM_001354616.2:c.316-4A>G
NM_001354617.2:c.316-4A>G
NM_001354618.2:c.316-4A>G
NM_001354619.2:c.316-4A>G
NM_001354620.2:c.745-4A>G
NM_001354621.2:c.16-4A>G
NM_001354622.2:c.16-4A>G
NM_001354623.2:c.16-4A>G
NM_001354624.2:c.-36-4A>G
NM_001354625.2:c.-36-4A>G
NM_001354626.2:c.-36-4A>G
NM_001354627.2:c.-36-4A>G
NM_001354628.2:c.1039-4A>G
NM_001354629.2:c.940-4A>G
NM_001354630.2:c.1039-4A>G
LRG_216t1:c.1039-4A>G
LRG_216:g.37284A>G
NC_000003.11:g.37067124A>G
NM_000249.3:c.1039-4A>G

Links:

dbSNP: rs368618417

NCBI 1000 Genomes Browser:

rs368618417

Molecular consequence:

NM_000249.4:c.1039-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001167617.3:c.745-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001167618.3:c.316-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001167619.3:c.316-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001258271.2:c.1039-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001258273.2:c.316-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001258274.3:c.316-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354615.2:c.316-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354616.2:c.316-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354617.2:c.316-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354618.2:c.316-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354619.2:c.316-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354620.2:c.745-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354621.2:c.16-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354622.2:c.16-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354623.2:c.16-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354624.2:c.-36-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354625.2:c.-36-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354626.2:c.-36-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354627.2:c.-36-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354628.2:c.1039-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354629.2:c.940-4A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354630.2:c.1039-4A>G - 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
SCV000785276	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Likely benign (Jun 23, 2017)	unknown	clinical testing	Counsyl_Autosomal_Dominant_Disease_Classification_criteria_(2015)_v1.pdf, Citation Link,
SCV004020280	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Likely benign (Mar 10, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000785276

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Likely benign
(Jun 23, 2017)

unknown

clinical testing

Counsyl_Autosomal_Dominant_Disease_Classification_criteria_(2015)_v1.pdf,

Citation Link,

SCV004020280

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Likely benign
(Mar 10, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Counsyl, SCV000785276.2

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

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

From Myriad Genetics, Inc., SCV004020280.1

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

Description

This variant is considered likely benign. This variant is intronic and is not expected to impact mRNA splicing.

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

Last Updated: Sep 29, 2024

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