NM_000179.3(MSH6):c.3802-40_3802-12del AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 2, 2021
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:: RCV001805526.2

Allele description [Variation Report for NM_000179.3(MSH6):c.3802-40_3802-12del]

NM_000179.3(MSH6):c.3802-40_3802-12del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.3802-40_3802-12del

HGVS:

NC_000002.12:g.47806412_47806440del
NG_007111.1:g.28266_28294del
NG_008397.1:g.104237_104265del
NM_000179.3:c.3802-40_3802-12delMANE SELECT
NM_001281492.2:c.3412-40_3412-12del
NM_001281493.2:c.2896-40_2896-12del
NM_001281494.2:c.2896-40_2896-12del
LRG_219t1:c.3802-40_3802-12del
LRG_219:g.28266_28294del
NC_000002.11:g.48033551_48033579del
NM_000179.2:c.3802-40_3802-12del

Links:

dbSNP: rs2104549153

NCBI 1000 Genomes Browser:

rs2104549153

Molecular consequence:

NM_000179.3:c.3802-40_3802-12del - intron variant - [Sequence Ontology: SO:0001627]
NM_001281492.2:c.3412-40_3412-12del - intron variant - [Sequence Ontology: SO:0001627]
NM_001281493.2:c.2896-40_2896-12del - intron variant - [Sequence Ontology: SO:0001627]
NM_001281494.2:c.2896-40_2896-12del - intron variant - [Sequence Ontology: SO:0001627]

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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LOC116747570 [Phocoena sinus]
LOC116747570 [Phocoena sinus]
Gene ID:116747570

Gene
Profile neighbors for GEO Profiles (Select 109436933) (80)
GEO Profiles
Chromosome neighbors for GEO Profiles (Select 109409692) (16)
GEO Profiles

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002053134	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jun 2, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002053134

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jun 2, 2021)

germline

clinical testing

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

Help

Summary from all submissions

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

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 Color Diagnostics, LLC DBA Color Health, SCV002053134.1

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

Description

This variant causes a deletion of 29 nucleotides between positions -40 and -12 in intron 8 of the MSH6 gene. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#	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: Dec 24, 2023

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