NM_000535.7(PMS2):c.1144+9A>C AND Hereditary nonpolyposis colorectal neoplasms

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely benign (1 submission)
Last evaluated:: Sep 25, 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:: RCV002152248.5

Allele description

NM_000535.7(PMS2):c.1144+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.1144+9A>C

HGVS:

NC_000007.14:g.5989791T>G
NG_008466.1:g.24316A>C
NM_000535.7:c.1144+9A>CMANE SELECT
NM_001322003.2:c.739+9A>C
NM_001322004.2:c.739+9A>C
NM_001322005.2:c.739+9A>C
NM_001322006.2:c.989-2171A>C
NM_001322007.2:c.826+9A>C
NM_001322008.2:c.826+9A>C
NM_001322009.2:c.739+9A>C
NM_001322010.2:c.584-2171A>C
NM_001322011.2:c.211+9A>C
NM_001322012.2:c.211+9A>C
NM_001322013.2:c.571+9A>C
NM_001322014.2:c.1144+9A>C
NM_001322015.2:c.835+9A>C
LRG_161:g.24316A>C
NC_000007.13:g.6029422T>G

Links:

dbSNP: rs2128746726

NCBI 1000 Genomes Browser:

rs2128746726

Molecular consequence:

NM_000535.7:c.1144+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322003.2:c.739+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322004.2:c.739+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322005.2:c.739+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322006.2:c.989-2171A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322007.2:c.826+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.826+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322009.2:c.739+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.584-2171A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322011.2:c.211+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322012.2:c.211+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322013.2:c.571+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322014.2:c.1144+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001322015.2:c.835+9A>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Hereditary nonpolyposis colorectal neoplasms
Identifiers:: MeSH: D003123; MedGen: C0009405

Recent activity

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Tonicella marmorea voucher ZMMU_MSU_WS19218 histone H3 gene, partial cds
Tonicella marmorea voucher ZMMU_MSU_WS19218 histone H3 gene, partial cds
gi|2571258528|gb|OR161100.1|

Nucleotide
Antennarius multiocellatus voucher TOB9336 cytochrome oxidase subunit 1 (COI) ge...
Antennarius multiocellatus voucher TOB9336 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial
gi|393005540|gnl|uoguelph|TOBA336-0 -5P|gb|JQ842784.1|

Nucleotide
Tonicella marmorea voucher WS848 small subunit ribosomal RNA gene, partial seque...
Tonicella marmorea voucher WS848 small subunit ribosomal RNA gene, partial sequence
gi|1646227648|gb|MK922030.1|

Nucleotide
Homo sapiens
Homo sapiens
Che-1/AATF sustains cell growth and global transcription in Multiple Myeloma through the maintenance of open chromatin structure [RNA-Seq]

BioProject
RecName: Full=Sphingomyelin phosphodiesterase 4; AltName: Full=Neutral sphingomy...
RecName: Full=Sphingomyelin phosphodiesterase 4; AltName: Full=Neutral sphingomyelinase 3; Short=nSMase-3; Short=nSMase3; AltName: Full=Neutral sphingomyelinase III
gi|82187187|sp|Q6PFJ7.1|NSMA3_DANRE

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002418946	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Sep 25, 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

SCV002418946

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Sep 25, 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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002418946.3

#	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: Feb 20, 2024

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