NM_000249.4(MLH1):c.1990-6G>A AND Lynch syndrome II

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: May 28, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000663093.2

Allele description [Variation Report for NM_000249.4(MLH1):c.1990-6G>A]

NM_000249.4(MLH1):c.1990-6G>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.1990-6G>A
HGVS:
  • NC_000003.12:g.37048898G>A
  • NG_007109.2:g.60549G>A
  • NM_000249.4:c.1990-6G>AMANE SELECT
  • NM_001167617.3:c.1696-6G>A
  • NM_001167618.3:c.1267-6G>A
  • NM_001167619.3:c.1267-6G>A
  • NM_001258271.2:c.1896+1215G>A
  • NM_001258273.2:c.1267-6G>A
  • NM_001258274.3:c.1267-6G>A
  • NM_001354615.2:c.1267-6G>A
  • NM_001354616.2:c.1267-6G>A
  • NM_001354617.2:c.1267-6G>A
  • NM_001354618.2:c.1267-6G>A
  • NM_001354619.2:c.1267-6G>A
  • NM_001354620.2:c.1696-6G>A
  • NM_001354621.2:c.967-6G>A
  • NM_001354622.2:c.967-6G>A
  • NM_001354623.2:c.967-6G>A
  • NM_001354624.2:c.916-6G>A
  • NM_001354625.2:c.916-6G>A
  • NM_001354626.2:c.916-6G>A
  • NM_001354627.2:c.916-6G>A
  • NM_001354628.2:c.1897-6G>A
  • NM_001354629.2:c.1891-6G>A
  • NM_001354630.2:c.1825-6G>A
  • LRG_216t1:c.1990-6G>A
  • LRG_216:g.60549G>A
  • NC_000003.11:g.37090389G>A
  • NM_000249.3:c.1990-6G>A
Links:
dbSNP: rs117221851
NCBI 1000 Genomes Browser:
rs117221851
Molecular consequence:
  • NM_000249.4:c.1990-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167617.3:c.1696-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167618.3:c.1267-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001167619.3:c.1267-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258271.2:c.1896+1215G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258273.2:c.1267-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258274.3:c.1267-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354615.2:c.1267-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354616.2:c.1267-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354617.2:c.1267-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354618.2:c.1267-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354619.2:c.1267-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354620.2:c.1696-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354621.2:c.967-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354622.2:c.967-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354623.2:c.967-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354624.2:c.916-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354625.2:c.916-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354626.2:c.916-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354627.2:c.916-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354628.2:c.1897-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354629.2:c.1891-6G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354630.2:c.1825-6G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Lynch syndrome II (HNPCC2)
Synonyms:
COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 2; MLH1-Related Hereditary Non-Polyposis Colon Cancer; MLH1-Related Lynch Syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012249; MedGen: C1333991; Orphanet: 144; OMIM: 609310

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000786196Counsylcriteria provided, single submitter
Uncertain significance
(Mar 15, 2018)
unknownclinical testing

Counsyl_Autosomal_Dominant_Disease_Classification_criteria_(2015)_v1.pdf,

Citation Link,

SCV001136432Mendelicscriteria provided, single submitter
Likely benign
(May 28, 2019)
unknownclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Counsyl, SCV000786196.2

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

From Mendelics, SCV001136432.1

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

Last Updated: Nov 27, 2021

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