NM_000152.5(GAA):c.1076-22T>G AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Sep 20, 2021
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:: RCV001570177.7

Allele description [Variation Report for NM_000152.5(GAA):c.1076-22T>G]

NM_000152.5(GAA):c.1076-22T>G

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.1076-22T>G

HGVS:

NC_000017.11:g.80108467T>G
NG_009822.1:g.11912T>G
NM_000152.5:c.1076-22T>GMANE SELECT
NM_001079803.3:c.1076-22T>G
NM_001079804.3:c.1076-22T>G
LRG_673t1:c.1076-22T>G
LRG_673:g.11912T>G
NC_000017.10:g.78082266T>G
NM_000152.3:c.1076-22T>G
NM_000152.4(GAA):c.1076-22T>G

Links:

dbSNP: rs762260678

NCBI 1000 Genomes Browser:

rs762260678

Molecular consequence:

NM_000152.5:c.1076-22T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001079803.3:c.1076-22T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001079804.3:c.1076-22T>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001794408	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Oct 29, 2019)	germline	clinical testing	Citation Link,
SCV002023834	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 20, 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

SCV001794408

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Oct 29, 2019)

germline

clinical testing

Citation Link,

SCV002023834

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 20, 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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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 GeneDx, SCV001794408.1

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

Description

Predicted to create a strong cryptic splice acceptor site upstream of the natural splice acceptor site of intron 6 and analysis of patient cDNA demonstrates an in-frame insertion of 21 nucleotides and skipping of exon 6 causing insertion of 7 incorrect amino acids and loss of 40 amino acids encoded by exon 6 (Adams et al., 1997; Vorgerd et al., 1998); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 31342611, 29181627, 9259196, 22613277, 10737124, 17643989, 21179066, 21484825, 27408821, 22676651, 25455803, 23013746, 9529346)

#	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 Revvity Omics, Revvity, SCV002023834.3

#	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: Sep 29, 2024

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