NM_000179.3(MSH6):c.3557-8_3557-4del AND Hereditary cancer-predisposing syndrome

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: May 24, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV002257124.3

Allele description [Variation Report for NM_000179.3(MSH6):c.3557-8_3557-4del]

NM_000179.3(MSH6):c.3557-8_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.3557-8_3557-4del

HGVS:

NC_000002.12:g.47805610_47805614del
NG_007111.1:g.27464_27468del
NG_008397.1:g.105070_105074del
NM_000179.3:c.3557-8_3557-4delMANE SELECT
NM_001281492.2:c.3167-8_3167-4del
NM_001281493.2:c.2651-8_2651-4del
NM_001281494.2:c.2651-8_2651-4del
LRG_219t1:c.3557-8_3557-4del
LRG_219:g.27464_27468del
NC_000002.11:g.48032749_48032753del
NM_000179.2:c.3557-8_3557-4del
NM_000179.2:c.3557-8_3557-4delTTTTT

Links:

dbSNP: rs267608102

NCBI 1000 Genomes Browser:

rs267608102

Molecular consequence:

NM_000179.3:c.3557-8_3557-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001281492.2:c.3167-8_3167-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001281493.2:c.2651-8_2651-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001281494.2:c.2651-8_2651-4del - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002528046	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Uncertain significance (Oct 6, 2021)	germline	curation	Citation Link,
SCV005145589	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (May 24, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002528046

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Uncertain significance
(Oct 6, 2021)

germline

curation

Citation Link,

SCV005145589

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(May 24, 2024)

germline

clinical testing

Citation Link

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, curation

Details of each submission

From Sema4, Sema4, SCV002528046.1

#	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

From Ambry Genetics, SCV005145589.1

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 11, 2024

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