NM_013296.5(GPSM2):c.278+5T>C AND not specified

Germline classification:: Benign (2 submissions)
Last evaluated:: Mar 14, 2016
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:: RCV000038783.6

Allele description [Variation Report for NM_013296.5(GPSM2):c.278+5T>C]

NM_013296.5(GPSM2):c.278+5T>C

Gene:

GPSM2:G protein signaling modulator 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p13.3

Genomic location:

Preferred name:

NM_013296.5(GPSM2):c.278+5T>C

HGVS:

NC_000001.11:g.108897090T>C
NG_028108.2:g.26741T>C
NM_001321038.2:c.278+5T>C
NM_001321039.3:c.278+5T>C
NM_013296.5:c.278+5T>CMANE SELECT
LRG_1373t1:c.278+5T>C
LRG_1373:g.26741T>C
NC_000001.10:g.109439712T>C
NM_013296.4:c.278+5T>C
c.278+5T>C

Links:

dbSNP: rs9727773

NCBI 1000 Genomes Browser:

rs9727773

Molecular consequence:

NM_001321038.2:c.278+5T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001321039.3:c.278+5T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_013296.5:c.278+5T>C - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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HD domain-containing protein [Paenimyroides ceti]
HD domain-containing protein [Paenimyroides ceti]
gi|2532951429|ref|WP_290361833.1|

Protein
c-type cytochrome [Paenimyroides ceti]
c-type cytochrome [Paenimyroides ceti]
gi|2532951431|ref|WP_290361835.1|

Protein
hypothetical protein [Paenimyroides ceti]
hypothetical protein [Paenimyroides ceti]
gi|2532954899|ref|WP_290365303.1|

Protein
OsmC family protein [Paenimyroides ceti]
OsmC family protein [Paenimyroides ceti]
gi|2532952687|ref|WP_290363091.1|

Protein
ARF GTPase-activating protein GIT2 isoform 21 [Mus musculus]
ARF GTPase-activating protein GIT2 isoform 21 [Mus musculus]
gi|2711571206|ref|NP_001416003.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000062461	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (May 7, 2012)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000521945	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Mar 14, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000062461

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(May 7, 2012)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000521945

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(Mar 14, 2016)

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	not provided	32	32	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000062461.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	32	not provided	not provided	clinical testing	PubMed (1)

Description

278+5T>C in Intron 03 of GPSM2: This variant is not expected to have clinical si gnificance because it has been identified in 10.3% (384/3738) of African America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs9727773).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		32	not provided	32	not provided

From GeneDx, SCV000521945.4

#	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

Last Updated: Sep 29, 2024

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