NM_000535.7(PMS2):c.353+9A>C AND not specified

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: May 29, 2018
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:: RCV000127471.16

Allele description [Variation Report for NM_000535.7(PMS2):c.353+9A>C]

NM_000535.7(PMS2):c.353+9A>C

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.353+9A>C

HGVS:

NC_000007.14:g.6003681T>G
NG_008466.1:g.10426A>C
NM_000535.7:c.353+9A>CMANE SELECT
NM_001322003.2:c.-53+9A>C
NM_001322004.2:c.-53+9A>C
NM_001322005.2:c.-53+9A>C
NM_001322006.2:c.353+9A>C
NM_001322007.2:c.35+291A>C
NM_001322008.2:c.35+291A>C
NM_001322009.2:c.-53+9A>C
NM_001322010.2:c.-53+9A>C
NM_001322011.2:c.-532+9A>C
NM_001322012.2:c.-532+9A>C
NM_001322013.2:c.-53+9A>C
NM_001322014.2:c.353+9A>C
NM_001322015.2:c.-132+9A>C
LRG_161t1:c.353+9A>C
LRG_161:g.10426A>C
NC_000007.13:g.6043312T>G
NM_000535.5:c.353+9A>C
NM_000535.6:c.353+9A>C

Links:

dbSNP: rs139990791

NCBI 1000 Genomes Browser:

rs139990791

Molecular consequence:

NM_000535.7:c.353+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322003.2:c.-53+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322004.2:c.-53+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322005.2:c.-53+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322006.2:c.353+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322007.2:c.35+291A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.35+291A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322009.2:c.-53+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-53+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322011.2:c.-532+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322012.2:c.-532+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322013.2:c.-53+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322014.2:c.353+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322015.2:c.-132+9A>C - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Mus musculus jumonji C domain-containing histone demethylase 1 homolog D (S. cer...
Mus musculus jumonji C domain-containing histone demethylase 1 homolog D (S. cerevisiae), mRNA (cDNA clone IMAGE:3488682), partial cds
gi|13938092|gb|BC007161.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000171044	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (May 23, 2014)	germline	clinical testing	Citation Link,
SCV000596474	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jan 12, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000806216	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Dec 30, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000861357	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Likely benign (May 29, 2018)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	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 GeneDx, SCV000171044.11

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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

From Genetic Services Laboratory, University of Chicago, SCV000596474.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000806216.1

#	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 Eurofins Ntd Llc (ga), SCV000861357.1

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

Last Updated: Sep 29, 2024

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