NM_000249.4(MLH1):c.116+4C>A AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 20, 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:: RCV001855740.4

Allele description [Variation Report for NM_000249.4(MLH1):c.116+4C>A]

NM_000249.4(MLH1):c.116+4C>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.116+4C>A

HGVS:

NC_000003.12:g.36993667C>A
NG_007109.2:g.5318C>A
NG_008418.1:g.4638G>T
NM_000249.4:c.116+4C>AMANE SELECT
NM_001167617.3:c.-397C>A
NM_001167618.3:c.-826C>A
NM_001167619.3:c.-739C>A
NM_001258271.2:c.116+4C>A
NM_001258273.2:c.-517+4C>A
NM_001258274.3:c.-976C>A
NM_001354615.2:c.-511+4C>A
NM_001354616.2:c.-511+4C>A
NM_001354617.2:c.-603+4C>A
NM_001354618.2:c.-831C>A
NM_001354619.2:c.-955C>A
NM_001354620.2:c.-169+4C>A
NM_001354621.2:c.-924C>A
NM_001354622.2:c.-1037C>A
NM_001354623.2:c.-946C>A
NM_001354624.2:c.-711+4C>A
NM_001354625.2:c.-609+4C>A
NM_001354626.2:c.-706+4C>A
NM_001354627.2:c.-934C>A
NM_001354628.2:c.116+4C>A
NM_001354629.2:c.116+4C>A
NM_001354630.2:c.116+4C>A
LRG_216t1:c.116+4C>A
LRG_216:g.5318C>A
NC_000003.11:g.37035158C>A
NM_000249.3:c.116+4C>A

Links:

dbSNP: rs1057523910

NCBI 1000 Genomes Browser:

rs1057523910

Molecular consequence:

NM_001167617.3:c.-397C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167618.3:c.-826C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-739C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-976C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-831C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-955C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-924C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-1037C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-946C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-934C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.116+4C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001258271.2:c.116+4C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001258273.2:c.-517+4C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354615.2:c.-511+4C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354616.2:c.-511+4C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354617.2:c.-603+4C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354620.2:c.-169+4C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354624.2:c.-711+4C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354625.2:c.-609+4C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354626.2:c.-706+4C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354628.2:c.116+4C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354629.2:c.116+4C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354630.2:c.116+4C>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002228336	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 20, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17576681, 9536098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002228336

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 20, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002228336.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change falls in intron 1 of the MLH1 gene. It does not directly change the encoded amino acid sequence of the MLH1 protein. It affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with MLH1-related conditions. ClinVar contains an entry for this variant (Variation ID: 628023). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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. 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.

#	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: Sep 29, 2024

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