NM_000179.3(MSH6):c.3554_3556+2del AND Lynch syndrome 5

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 24, 2023
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:: RCV003449999.1

Allele description [Variation Report for NM_000179.3(MSH6):c.3554_3556+2del]

NM_000179.3(MSH6):c.3554_3556+2del

Gene:

MSH6:mutS homolog 6 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.3554_3556+2del

HGVS:

NC_000002.12:g.47805025_47805029del
NG_007111.1:g.26879_26883del
NG_008397.1:g.105649_105653del
NM_000179.3:c.3554_3556+2delMANE SELECT
NM_001281492.2:c.3164_3166+2del
NM_001281493.2:c.2648_2650+2del
NM_001281494.2:c.2648_2650+2del
LRG_219:g.26879_26883del
NC_000002.11:g.48032164_48032168del

Links:

dbSNP: rs2104510085

NCBI 1000 Genomes Browser:

rs2104510085

Molecular consequence:

NM_000179.3:c.3554_3556+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001281492.2:c.3164_3166+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001281493.2:c.2648_2650+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001281494.2:c.2648_2650+2del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Lynch syndrome 5 (LYNCH5)
Synonyms:: Colorectal cancer, hereditary nonpolyposis, type 5; Hereditary non-polyposis colorectal cancer, type 5
Identifiers:: MONDO: MONDO:0013710; MedGen: C1833477; Orphanet: 144; OMIM: 614350

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004189313	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Likely pathogenic (Aug 24, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004189313

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Likely pathogenic
(Aug 24, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Myriad Genetics, Inc., SCV004189313.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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