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NM_000249.4(MLH1):c.114C>T (p.Asn38=) AND not specified

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jul 12, 2019
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:
RCV001192577.1

Allele description [Variation Report for NM_000249.4(MLH1):c.114C>T (p.Asn38=)]

NM_000249.4(MLH1):c.114C>T (p.Asn38=)

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.114C>T (p.Asn38=)
HGVS:
  • NC_000003.12:g.36993661C>T
  • NG_007109.2:g.5312C>T
  • NG_008418.1:g.4644G>A
  • NM_000249.4:c.114C>TMANE SELECT
  • NM_001167617.3:c.-403C>T
  • NM_001167618.3:c.-832C>T
  • NM_001167619.3:c.-745C>T
  • NM_001258271.2:c.114C>T
  • NM_001258273.2:c.-519C>T
  • NM_001258274.3:c.-982C>T
  • NM_001354615.2:c.-513C>T
  • NM_001354616.2:c.-513C>T
  • NM_001354617.2:c.-605C>T
  • NM_001354618.2:c.-837C>T
  • NM_001354619.2:c.-961C>T
  • NM_001354620.2:c.-171C>T
  • NM_001354621.2:c.-930C>T
  • NM_001354622.2:c.-1043C>T
  • NM_001354623.2:c.-952C>T
  • NM_001354624.2:c.-713C>T
  • NM_001354625.2:c.-611C>T
  • NM_001354626.2:c.-708C>T
  • NM_001354627.2:c.-940C>T
  • NM_001354628.2:c.114C>T
  • NM_001354629.2:c.114C>T
  • NM_001354630.2:c.114C>T
  • NP_000240.1:p.Asn38=
  • NP_000240.1:p.Asn38=
  • NP_001245200.1:p.Asn38=
  • NP_001341557.1:p.Asn38=
  • NP_001341558.1:p.Asn38=
  • NP_001341559.1:p.Asn38=
  • LRG_216t1:c.114C>T
  • LRG_216:g.5312C>T
  • LRG_216p1:p.Asn38=
  • NC_000003.11:g.37035152C>T
  • NM_000249.3:c.114C>T
Links:
dbSNP: rs267607706
NCBI 1000 Genomes Browser:
rs267607706
Molecular consequence:
  • NM_001167617.3:c.-403C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167618.3:c.-832C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167619.3:c.-745C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258273.2:c.-519C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258274.3:c.-982C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354615.2:c.-513C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354616.2:c.-513C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354617.2:c.-605C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354618.2:c.-837C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354619.2:c.-961C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354620.2:c.-171C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354621.2:c.-930C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354622.2:c.-1043C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354623.2:c.-952C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354624.2:c.-713C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354625.2:c.-611C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354626.2:c.-708C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354627.2:c.-940C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000249.4:c.114C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001258271.2:c.114C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354628.2:c.114C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354629.2:c.114C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354630.2:c.114C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001360805Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely benign
(Jul 12, 2019) 		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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001360805.1

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

Description

Variant summary: MLH1 c.114C>T (p.Asn38Asn) alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4e-06 in 250316 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.114C>T in individuals affected with Hereditary Non-Polyposis Colon Cancer and no experimental evidence demonstrating its impact on protein function have been reported. Two ClinVar submissions from other clinical diagnostic laboratories (evaluation after 2014) cite the variant as likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

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

Last Updated: Oct 8, 2024