NM_000179.3(MSH6):c.3557-4del AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Sep 29, 2021
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:: RCV000162386.13

Allele description [Variation Report for NM_000179.3(MSH6):c.3557-4del]

NM_000179.3(MSH6):c.3557-4del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.3557-4del

HGVS:

NC_000002.12:g.47805614del
NG_007111.1:g.27468del
NG_008397.1:g.105074del
NM_000179.2:c.3557-12delT
NM_000179.3:c.3557-4delMANE SELECT
NM_001281492.2:c.3167-4del
NM_001281493.2:c.2651-4del
NM_001281494.2:c.2651-4del
LRG_219t1:c.3557-4del
LRG_219:g.27468del
NC_000002.11:g.48032741delT
NC_000002.11:g.48032753del
NM_000179.2:c.3557-12delT
NM_000179.2:c.3557-16delT
NM_000179.2:c.3557-4del
NM_000179.2:c.3557-4delT
NM_000179.3:c.3557-4delTMANE SELECT

Links:

dbSNP: rs267608102

NCBI 1000 Genomes Browser:

rs267608102

Molecular consequence:

NM_000179.3:c.3557-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001281492.2:c.3167-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001281493.2:c.2651-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001281494.2:c.2651-4del - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000212699	Ambry Genetics	criteria provided, single submitter (Ambry Autosomal Dominant and X-Linked criteria (3/2017))	Likely benign (Mar 20, 2018)	germline	clinical testing	Citation Link,
SCV000911650	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Apr 8, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002528042	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Benign (Sep 29, 2021)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000212699

Ambry Genetics

criteria provided, single submitter

(Ambry Autosomal Dominant and X-Linked criteria (3/2017))

Likely benign
(Mar 20, 2018)

germline

clinical testing

Citation Link,

SCV000911650

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Apr 8, 2015)

germline

clinical testing

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

SCV002528042

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Benign
(Sep 29, 2021)

germline

curation

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	not provided	not provided	1	not provided	clinical testing, curation

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Ambry Genetics, SCV000212699.6

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

Description

This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

From Color Diagnostics, LLC DBA Color Health, SCV000911650.1

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

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

From Sema4, Sema4, SCV002528042.1

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

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

Last Updated: Jun 9, 2024

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