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NM_000249.4(MLH1):c.1039-3C>T AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Feb 20, 2024
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:
RCV000213179.4

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)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000279423GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Uncertain significance
(Feb 20, 2024) 		germlineclinical testing

Citation Link,

SCV002774616Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)		Uncertain significance
(Aug 4, 2021) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From GeneDx, SCV000279423.11

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this variant does not alter splicing; Has not been previously published as pathogenic or benign to our knowledge

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002774616.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024