NM_000249.4(MLH1):c.884+16A>G AND not provided

Clinical significance:Uncertain significance (Last evaluated: Jan 7, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_000249.4(MLH1):c.884+16A>G]


MLH1:mutL homolog 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
  • NC_000003.12:g.37017615A>G
  • NG_007109.2:g.29266A>G
  • NM_000249.3:c.884+16A>G
  • NM_000249.4:c.884+16A>GMANE SELECT
  • NM_001167617.3:c.590+16A>G
  • NM_001167618.3:c.161+16A>G
  • NM_001167619.3:c.161+16A>G
  • NM_001258271.2:c.884+16A>G
  • NM_001258273.2:c.161+16A>G
  • NM_001258274.3:c.161+16A>G
  • NM_001354615.2:c.161+16A>G
  • NM_001354616.2:c.161+16A>G
  • NM_001354617.2:c.161+16A>G
  • NM_001354618.2:c.161+16A>G
  • NM_001354619.2:c.161+16A>G
  • NM_001354620.2:c.590+16A>G
  • NM_001354621.2:c.-139-2695A>G
  • NM_001354622.2:c.-139-2695A>G
  • NM_001354623.2:c.-139-2695A>G
  • NM_001354624.2:c.-37+3071A>G
  • NM_001354625.2:c.-37+3071A>G
  • NM_001354626.2:c.-37+3071A>G
  • NM_001354627.2:c.-37+3071A>G
  • NM_001354628.2:c.884+16A>G
  • NM_001354629.2:c.785+16A>G
  • NM_001354630.2:c.884+16A>G
  • LRG_216t1:c.884+16A>G
  • LRG_216:g.29266A>G
  • NC_000003.11:g.37059106A>G
dbSNP: rs377598055
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000249.3:c.884+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000249.4:c.884+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167617.3:c.590+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167618.3:c.161+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167619.3:c.161+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258271.2:c.884+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258273.2:c.161+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258274.3:c.161+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354615.2:c.161+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354616.2:c.161+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354617.2:c.161+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354618.2:c.161+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354619.2:c.161+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354620.2:c.590+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354621.2:c.-139-2695A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354622.2:c.-139-2695A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354623.2:c.-139-2695A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354624.2:c.-37+3071A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354625.2:c.-37+3071A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354626.2:c.-37+3071A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354627.2:c.-37+3071A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354628.2:c.884+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354629.2:c.785+16A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354630.2:c.884+16A>G - intron variant - [Sequence Ontology: SO:0001627]


MedGen: CN517202

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000696186Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Uncertain significance
(Jan 7, 2016)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001808104Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensusno assertion criteria providedLikely benigngermlineclinical testing

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696186.1

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


Variant summary: This c.884+16A>G variant affects a non-conserved nucleotide, resulting in intronic change at a position not widely known to affect normal splicing. 4/5 splice-site tools via Alamut predict that this variant does not affect normal splicing. ESEfinder also predicts the variant not to affect any ESE binding sites. This variant was found in 22/121388 chromosomes from the broad and large populations of ExAC at a frequency of 0.0001812. It was mainly found in the European Non-Finnish sub-population where its allele frequency is 0.0003 (20/66728 chromosomes), which, albeit is lower than the maximal expected allele frequency in this gene (0.0007105), suggests that it might be a rare polymorphism in this population. To our knowledge, the variant has not been reported in affected individuals via publications and/or reputable databases/clinical laboratories; nor evaluated for functional impact by in vivo/vitro studies. One clinical lab has classified this variant as benign. Taken together, this variant has currently been classified as VUS-possibly benign.

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

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001808104.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 6, 2021

Support Center