NM_000535.7(PMS2):c.706-4del AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign (2 submissions)
Last evaluated:: Oct 6, 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:: RCV000564416.7

Allele description [Variation Report for NM_000535.7(PMS2):c.706-4del]

NM_000535.7(PMS2):c.706-4del

Gene:

PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.706-4del

HGVS:

NC_000007.13:g.6037058del
NC_000007.14:g.5997443del
NG_008466.1:g.16680del
NM_000535.7:c.706-4delMANE SELECT
NM_001322003.2:c.301-4del
NM_001322004.2:c.301-4del
NM_001322005.2:c.301-4del
NM_001322006.2:c.706-4del
NM_001322007.2:c.388-4del
NM_001322008.2:c.388-4del
NM_001322009.2:c.301-4del
NM_001322010.2:c.301-4del
NM_001322011.2:c.-228-4del
NM_001322012.2:c.-228-4del
NM_001322013.2:c.133-4del
NM_001322014.2:c.706-4del
NM_001322015.2:c.397-4del
LRG_161t1:c.706-4del
LRG_161:g.16680del
NC_000007.13:g.6037058del
NC_000007.13:g.6037058delA
NC_000007.13:g.6037074del
NM_000535.5:c.706-4del
NM_000535.5:c.706-4delT
NM_000535.5:c.706-5delT
NM_000535.6:c.706-4delT
NM_000535.6:c.706-5del
NM_000535.6:c.706-5delT
NM_000535.5:c.706-4delT

Links:

Ambry Genetics: a02961; dbSNP: rs60794673

NCBI 1000 Genomes Browser:

rs60794673

Molecular consequence:

NM_000535.7:c.706-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322003.2:c.301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322004.2:c.301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322005.2:c.301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322006.2:c.706-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322007.2:c.388-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.388-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322009.2:c.301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.301-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322011.2:c.-228-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322012.2:c.-228-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322013.2:c.133-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322014.2:c.706-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322015.2:c.397-4del - 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
SCV000663426	Ambry Genetics	criteria provided, single submitter (Ambry Autosomal Dominant and X-Linked criteria (3/2017))	Benign (May 18, 2017)	germline	clinical testing	Citation Link,
SCV000691102	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Oct 6, 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

SCV000663426

Ambry Genetics

criteria provided, single submitter

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

Benign
(May 18, 2017)

germline

clinical testing

Citation Link,

SCV000691102

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Oct 6, 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	1	not provided	not provided	1	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 Ambry Genetics, SCV000663426.4

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

Description

General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance

#	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, SCV000691102.3

#	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

Last Updated: Sep 29, 2024

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