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

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 20, 2024
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:
RCV000566363.4

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

NM_000249.4(MLH1):c.1039-3C>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.1039-3C>T
HGVS:
  • NC_000003.12:g.37025634C>T
  • NG_007109.2:g.37285C>T
  • NM_000249.4:c.1039-3C>TMANE SELECT
  • NM_001167617.3:c.745-3C>T
  • NM_001167618.3:c.316-3C>T
  • NM_001167619.3:c.316-3C>T
  • NM_001258271.2:c.1039-3C>T
  • NM_001258273.2:c.316-3C>T
  • NM_001258274.3:c.316-3C>T
  • NM_001354615.2:c.316-3C>T
  • NM_001354616.2:c.316-3C>T
  • NM_001354617.2:c.316-3C>T
  • NM_001354618.2:c.316-3C>T
  • NM_001354619.2:c.316-3C>T
  • NM_001354620.2:c.745-3C>T
  • NM_001354621.2:c.16-3C>T
  • NM_001354622.2:c.16-3C>T
  • NM_001354623.2:c.16-3C>T
  • NM_001354624.2:c.-36-3C>T
  • NM_001354625.2:c.-36-3C>T
  • NM_001354626.2:c.-36-3C>T
  • NM_001354627.2:c.-36-3C>T
  • NM_001354628.2:c.1039-3C>T
  • NM_001354629.2:c.940-3C>T
  • NM_001354630.2:c.1039-3C>T
  • LRG_216t1:c.1039-3C>T
  • LRG_216:g.37285C>T
  • NC_000003.11:g.37067125C>T
  • NM_000249.3:c.1039-3C>T
  • NM_001167618.1:c.316-3C>T
Links:
dbSNP: rs730881737
NCBI 1000 Genomes Browser:
rs730881737
Molecular consequence:
  • NM_000249.4:c.1039-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167617.3:c.745-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167618.3:c.316-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167619.3:c.316-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258271.2:c.1039-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258273.2:c.316-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258274.3:c.316-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354615.2:c.316-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354616.2:c.316-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354617.2:c.316-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354618.2:c.316-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354619.2:c.316-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354620.2:c.745-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354621.2:c.16-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354622.2:c.16-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354623.2:c.16-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354624.2:c.-36-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354625.2:c.-36-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354626.2:c.-36-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354627.2:c.-36-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354628.2:c.1039-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354629.2:c.940-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354630.2:c.1039-3C>T - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000669529Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Mar 20, 2024) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV000669529.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.1039-3C>T intronic variant results from a C to T substitution 3 nucleotides upstream from coding exon 12 in the MLH1 gene. This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing; however, direct evidence is insufficient at this time (Ambry internal data). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

Last Updated: Sep 29, 2024