NM_000249.4(MLH1):c.1039-3C>A AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 17, 2017
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:: RCV002396941.2

Allele description [Variation Report for NM_000249.4(MLH1):c.1039-3C>A]

NM_000249.4(MLH1):c.1039-3C>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.1039-3C>A

HGVS:

NC_000003.12:g.37025634C>A
NG_007109.2:g.37285C>A
NM_000249.4:c.1039-3C>AMANE SELECT
NM_001167617.3:c.745-3C>A
NM_001167618.3:c.316-3C>A
NM_001167619.3:c.316-3C>A
NM_001258271.2:c.1039-3C>A
NM_001258273.2:c.316-3C>A
NM_001258274.3:c.316-3C>A
NM_001354615.2:c.316-3C>A
NM_001354616.2:c.316-3C>A
NM_001354617.2:c.316-3C>A
NM_001354618.2:c.316-3C>A
NM_001354619.2:c.316-3C>A
NM_001354620.2:c.745-3C>A
NM_001354621.2:c.16-3C>A
NM_001354622.2:c.16-3C>A
NM_001354623.2:c.16-3C>A
NM_001354624.2:c.-36-3C>A
NM_001354625.2:c.-36-3C>A
NM_001354626.2:c.-36-3C>A
NM_001354627.2:c.-36-3C>A
NM_001354628.2:c.1039-3C>A
NM_001354629.2:c.940-3C>A
NM_001354630.2:c.1039-3C>A
LRG_216t1:c.1039-3C>A
LRG_216:g.37285C>A
NC_000003.11:g.37067125C>A
NM_000249.3:c.1039-3C>A

Molecular consequence:

NM_000249.4:c.1039-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001167617.3:c.745-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001167618.3:c.316-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001167619.3:c.316-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001258271.2:c.1039-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001258273.2:c.316-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001258274.3:c.316-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354615.2:c.316-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354616.2:c.316-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354617.2:c.316-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354618.2:c.316-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354619.2:c.316-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354620.2:c.745-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354621.2:c.16-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354622.2:c.16-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354623.2:c.16-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354624.2:c.-36-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354625.2:c.-36-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354626.2:c.-36-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354627.2:c.-36-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354628.2:c.1039-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354629.2:c.940-3C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354630.2:c.1039-3C>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002697520	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (May 17, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002697520

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(May 17, 2017)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV002697520.2

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

Description

The c.1039-3C>A intronic variant results from a C to A substitution 3 nucleotides upstream from coding exon 12 in the MLH1 gene. This nucleotide position is well conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to weaken the efficiency of the native splice acceptor site; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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

Last Updated: May 1, 2024

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