NM_000152.5(GAA):c.2646+55G>T AND not provided

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jun 10, 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:: RCV000589352.2

Allele description [Variation Report for NM_000152.5(GAA):c.2646+55G>T]

NM_000152.5(GAA):c.2646+55G>T

Gene:

GAA:alpha glucosidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q25.3

Genomic location:

Preferred name:

NM_000152.5(GAA):c.2646+55G>T

HGVS:

NC_000017.11:g.80118412G>T
NG_009822.1:g.21857G>T
NM_000152.5:c.2646+55G>TMANE SELECT
NM_001079803.3:c.2646+55G>T
NM_001079804.3:c.2646+55G>T
LRG_673t1:c.2646+55G>T
LRG_673:g.21857G>T
NC_000017.10:g.78092211G>T
NM_000152.3:c.2646+55G>T

Links:

dbSNP: rs141765552

NCBI 1000 Genomes Browser:

rs141765552

Molecular consequence:

NM_000152.5:c.2646+55G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001079803.3:c.2646+55G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001079804.3:c.2646+55G>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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GRB2 growth factor receptor bound protein 2 [Homo sapiens]
GRB2 growth factor receptor bound protein 2 [Homo sapiens]
Gene ID:2885

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000695659	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Jun 10, 2016)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV005214237	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000695659

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(Jun 10, 2016)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV005214237

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign

germline

not provided

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	yes	not provided	not provided	not provided	not provided	not provided	not provided
not provided	germline	unknown	not provided	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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695659.1

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

Description

Variant summary: The c.2646+55G>T in GAA gene is an intronic variant that affects a non-conserved nucleotide located at a position not widely known to affect splicing. One in silico tool predicts a benign outcome for this variant. 5/5 in silico splicing tools predict no significant effects on splicing, however these predictions have yet to be confirmed by in vitro/vivo studies. This variant was found in 11/5008 control chromosomes from the 1000G control database (coverage of this region in ExAC was too low to be reliable), predominantly observed in the European subpopulation at a frequency of 0.0099 (10/1006). This frequency is over two times the estimated maximal expected allele frequency of a pathogenic GAA variant (0.0042205), suggesting this is likely a benign polymorphism found primarily in the populations of European origin. The variant was not reported in affected individuals in published reports or clinical diagnostic centers. Taken together, based on the prevalence in the general population and lack of a predicted effect on splicing, the variant was classified as Likely Benign.

#	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 Breakthrough Genomics, Breakthrough Genomics, SCV005214237.1

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

#	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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