NM_000535.7(PMS2):c.1144+250_2175-1948del AND Hepatocellular carcinoma

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 17, 2022
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV002280925.1

Allele description [Variation Report for NM_000535.7(PMS2):c.1144+250_2175-1948del]

NM_000535.7(PMS2):c.1144+250_2175-1948del

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.1144+250_2175-1948del

HGVS:

NC_000007.14:g.5980652_5989558del
NG_008466.1:g.24557_33463del
NM_000535.7:c.1144+250_2175-1948delMANE SELECT
NM_001322003.2:c.739+250_1770-1948del
NM_001322004.2:c.739+250_1770-1948del
NM_001322005.2:c.739+250_1770-1948del
NM_001322006.2:c.989-1930_2019-1948del
NM_001322007.2:c.826+250_1857-1948del
NM_001322008.2:c.826+250_1857-1948del
NM_001322009.2:c.739+250_1770-1948del
NM_001322010.2:c.584-1930_1614-1948del
NM_001322011.2:c.211+250_1242-1948del
NM_001322012.2:c.211+250_1242-1948del
NM_001322013.2:c.571+250_1602-1948del
NM_001322014.2:c.1144+250_2175-1948del
NM_001322015.2:c.835+250_1866-1948del
LRG_161:g.24557_33463del
NC_000007.13:g.6020283_6029189del

Molecular consequence:

NM_000535.7:c.1144+250_2175-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322003.2:c.739+250_1770-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322004.2:c.739+250_1770-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322005.2:c.739+250_1770-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322006.2:c.989-1930_2019-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322007.2:c.826+250_1857-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322008.2:c.826+250_1857-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322009.2:c.739+250_1770-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322010.2:c.584-1930_1614-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322011.2:c.211+250_1242-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322012.2:c.211+250_1242-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322013.2:c.571+250_1602-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322014.2:c.1144+250_2175-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322015.2:c.835+250_1866-1948del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_000535.7:c.1144+250_2175-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322003.2:c.739+250_1770-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322004.2:c.739+250_1770-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322005.2:c.739+250_1770-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322006.2:c.989-1930_2019-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322007.2:c.826+250_1857-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322008.2:c.826+250_1857-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322009.2:c.739+250_1770-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322010.2:c.584-1930_1614-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322011.2:c.211+250_1242-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322012.2:c.211+250_1242-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322013.2:c.571+250_1602-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322014.2:c.1144+250_2175-1948del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322015.2:c.835+250_1866-1948del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Hepatocellular carcinoma (HCC)
Synonyms:: Primary carcinoma of liver; Hepatoma; LIVER CELL CARCINOMA; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007256; MedGen: C2239176; OMIM: 114550; Human Phenotype Ontology: HP:0001402

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002569169	CZECANCA consortium	no assertion criteria provided	Likely pathogenic (May 17, 2022)	germline	case-control

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002569169

CZECANCA consortium

no assertion criteria provided

Likely pathogenic
(May 17, 2022)

germline

case-control

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	case-control

Details of each submission

From CZECANCA consortium, SCV002569169.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	case-control	not provided

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

Last Updated: Jul 29, 2023

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