rs368539333

Variant names:

• chr17-80108610-G-C
• rs368539333
• NM_000152.5:c.1194+3G>C

Your query was ambiguous. Multiple possible variants found:

• chr17-80108610-G-C
• chr17-80108610-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PP4_Moderate PM3 PM2_Supporting

This summary comes from the ClinGen Evidence Repository: The NM_000152.5:c.1194+3G>C variant in GAA is located in the donor splice site consensus region of intron 7. The variant has been identified in four individuals, three with documented laboratory values showing GAA activity in the affected range in dried blood spots (Clinical Diagnostic Laboratories, PMID:33073003). One of these individuals is reported to be symptomatic, with GAA activity in the affected range in dried blood spots, and absence of known pseudodeficiency variants (PP4_Moderate); this individual is compound heterozygous for the variant and another variant in GAA that has been classified as pathogenic by the ClinGen Lysosomal Diseases VCEP - c.1210G>A (p.Asp404Asn), ClinVar Variation ID: 657348, SCV002817441.1, confirmed in trans (Clinical Laboratory) (PM3). The other individuals were identified on newborn screen will not be included because it is unknown if they are clinically symptomatic or if the enzyme deficiency could be the result of pseudodeficiency. These individuals are compound heterozygous for the variant and either c.1781G>A (p.Arg594His) (in trans based on testing of one parent), ClinVar Variation ID: 972747; SCV002817431.1; c.1841C>A (p.Thr614Lys), ClinVar Variation ID: 167113, SCV001371751.1, phase unknown (Clinical Laboratory); or c.1827del (ClinVar Variation ID: 188936, SCV001371738.1) (Clinical Laboratory). The highest population minor allele frequency in gnomAD v2.1.1. is 0.0003149 (40/127034 alleles) in the European (non-Finnish) population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting). The computational predictor SpliceAI gives a score of 0.17 for loss of the intron 7 donor splice site, and a score of 0.31 for loss of the intron 6 acceptor splice site suggesting possible effect on splicing but not meeting the current SpliceAI threshold (>0.5) of the ClinGen Lysosomal Diseases VCEP (PP3 not met). There is a ClinVar entry for this variant (Variation ID: 198393). In summary, this variant meets the criteria to be classified as a variant of uncertain significance for Pompe disease. GAA-specific ACMG/AMP criteria met, as specified by the ClinGen Lysosomal Diseases VCEP (Specifications Version 2.0): PM3, PP4_Moderate, PM2_Supporting.(Classification approved by the ClinGen Lysosomal Diseases VCEP on May 21, 2024) LINK:https://erepo.genome.network/evrepo/ui/classification/CA247031/MONDO:0009290/010

• Frequency:
  • Genomes: 𝑓 0.000072 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00026 (0 hom.)
• Consequence: GAA NM_000152.5 splice_region, intron
• Scores: Splicing: ADA: 0.1642
• Clinical Significance: Uncertain significance reviewed by expert panel P:5 U:9 B:1
• Conservation: PhyloP100: 0.135

Genes affected

GAA (HGNC:4065): (alpha glucosidase) This gene encodes lysosomal alpha-glucosidase, which is essential for the degradation of glycogen to glucose in lysosomes. The encoded preproprotein is proteolytically processed to generate multiple intermediate forms and the mature form of the enzyme. Defects in this gene are the cause of glycogen storage disease II, also known as Pompe's disease, which is an autosomal recessive disorder with a broad clinical spectrum. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAA	NM_000152.5	c.1194+3G>C		splice_region_variant, intron_variant	Intron 7 of 19	ENST00000302262.8	NP_000143.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAA	ENST00000302262.8	c.1194+3G>C		splice_region_variant, intron_variant	Intron 7 of 19	1	NM_000152.5	ENSP00000305692.3

Frequencies

GnomAD3 genomes AF: 0.0000723 AC: 11 AN: 152216 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000723

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000169 AC: 42 AN: 247840 Hom.: 0 AF XY: 0.000171 AC XY: 23 AN XY: 134808

Gnomad AFR exome AF: 0.000126

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000546

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000340

Gnomad OTH exome AF: 0.000166

GnomAD4 exome AF: 0.000264 AC: 385 AN: 1460446 Hom.: 0 Cov.: 39 AF XY: 0.000241 AC XY: 175 AN XY: 726550

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000192

Gnomad4 NFE exome AF: 0.000332

Gnomad4 OTH exome AF: 0.000215

GnomAD4 genome AF: 0.0000723 AC: 11 AN: 152216 Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8 AN XY: 74358

Gnomad4 AFR AF: 0.0000723

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000103

Gnomad4 OTH AF: 0.000478

Alfa AF: 0.000201 Hom.: 0

Bravo AF: 0.0000642

EpiCase AF: 0.000218

EpiControl AF: 0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:5 Uncertain:9 Benign:1

Revision: reviewed by expert panel

Submissions by phenotype

Glycogen storage disease, type II Pathogenic:4 Uncertain:4

Sep 05, 2021

Genome-Nilou Lab

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 24, 2020

Natera, Inc.

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

May 21, 2024

ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel

Significance: Uncertain significance

Review Status: reviewed by expert panel

Collection Method: curation

The NM_000152.5:c.1194+3G>C variant in GAA is located in the donor splice site consensus region of intron 7. The variant has been identified in four individuals, three with documented laboratory values showing GAA activity in the affected range in dried blood spots (Clinical Diagnostic Laboratories, PMID: 33073003). One of these individuals is reported to be symptomatic, with GAA activity in the affected range in dried blood spots, and absence of known pseudodeficiency variants (PP4_Moderate); this individual is compound heterozygous for the variant and another variant in GAA that has been classified as pathogenic by the ClinGen Lysosomal Diseases VCEP - c.1210G>A (p.Asp404Asn), ClinVar Variation ID: 657348, SCV002817441.1, confirmed in trans (Clinical Laboratory) (PM3). The other individuals were identified on newborn screen will not be included because it is unknown if they are clinically symptomatic or if the enzyme deficiency could be the result of pseudodeficiency. These individuals are compound heterozygous for the variant and either c.1781G>A (p.Arg594His) (in trans based on testing of one parent), ClinVar Variation ID: 972747; SCV002817431.1; c.1841C>A (p.Thr614Lys), ClinVar Variation ID: 167113, SCV001371751.1, phase unknown (Clinical Laboratory); or c.1827del (ClinVar Variation ID: 188936, SCV001371738.1) (Clinical Laboratory). The highest population minor allele frequency in gnomAD v2.1.1. is 0.0003149 (40/127034 alleles) in the European (non-Finnish) population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting). The computational predictor SpliceAI gives a score of 0.17 for loss of the intron 7 donor splice site, and a score of 0.31 for loss of the intron 6 acceptor splice site suggesting possible effect on splicing but not meeting the current SpliceAI threshold (>0.5) of the ClinGen Lysosomal Diseases VCEP (PP3 not met). There is a ClinVar entry for this variant (Variation ID: 198393). In summary, this variant meets the criteria to be classified as a variant of uncertain significance for Pompe disease. GAA-specific ACMG/AMP criteria met, as specified by the ClinGen Lysosomal Diseases VCEP (Specifications Version 2.0): PM3, PP4_Moderate, PM2_Supporting. (Classification approved by the ClinGen Lysosomal Diseases VCEP on May 21, 2024) -

Jan 23, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 7 of the GAA gene. It does not directly change the encoded amino acid sequence of the GAA protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs368539333, gnomAD 0.03%). This variant has been observed in individual(s) with biochemical features of Pompe disease (PMID: 33073003, 33202836; External communication, internal data). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 198393). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -

Mar 25, 2024

Baylor Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 20, 2025

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

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: GAA c.1194+3G>C alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: One predict the variant abolishes the canonical 5' splicing donor site. Three predict the variant weakens the canonical 5' splicing donor site. Three predict the variant creates a new canonical 3' splicing acceptor site at intronic position +5. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00017 in 247840 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in GAA causing Glycogen Storage Disease, Type 2 (Pompe Disease) (0.00017 vs 0.0042), allowing no conclusion about variant significance. c.1194+3G>C has been observed in the literature during newborn screening in settings of low GAA activity and second pathogenic variants and biochemical features of Pompe disease and at our laboratory (Burton_2019, Ficicioglu_2020, internal data and external communication).These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 33073003, 33202836). ClinVar contains an entry for this variant (Variation ID: 198393). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Aug 17, 2023

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The GAA c.1194+3G>C variant (rs368539333) is reported in the literature in compound heterozygous individuals with reduced GAA activity identified by newborn screening (Burton 2020, Ficicioglu 2020). This variant is reported in ClinVar (Variation ID: 198393) and is found in the general population with an overall allele frequency of 0.0158% (44/279,222 alleles) in the Genome Aggregation Database. This is an intronic variant in a weakly conserved nucleotide, but computational analyses (Alamut Visual Plus v.1.5.1) predict that this variant may impact splicing by weakening the nearby canonical donor splice site. The c.1194+3G>C variant is classified as likely pathogenic by the ClinGen lysosomal diseases variant curation expert panel, however, internal data was cited and could not be independently verified. Due to limited information, the clinical significance of this variant is uncertain at this time. References: Link to lysosomal diseases VCEP: https://clinicalgenome.org/affiliation/50009 Burton BK et al. Newborn Screening for Pompe Disease in Illinois: Experience with 684,290 Infants. Int J Neonatal Screen. 2020 Jan 21;6(1):4. PMID: 33073003. Ficicioglu C et al. Newborn Screening for Pompe Disease: Pennsylvania Experience. Int J Neonatal Screen. 2020 Nov 13;6(4):89. PMID: 33202836. -

Feb 02, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Pathogenic:1 Uncertain:4 Benign:1

Oct 19, 2023

Revvity Omics, Revvity

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 22, 2015

Eurofins Ntd Llc (ga)

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Aug 20, 2024

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Identified with a second variant in GAA in individuals with slightly reduced GAA activity identified on newborn screening for GSDII; these individuals were not clinically symptomatic at the time of report (PMID: 33202836, 33073003); In silico analysis supports that this variant does not alter splicing; This variant is associated with the following publications: (PMID: 33073003, 37937776, 33202836) -

Feb 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

GAA: BP4 -

-

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

GAA-related disorder Uncertain:1

May 06, 2024

PreventionGenetics, part of Exact Sciences

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

The GAA c.1194+3G>C variant is predicted to interfere with splicing. This variant has been reported in the compound heterozygous state in two individuals with suspected Pompe disease identified via newborn screening (Burton et al. 2020. PubMed ID: 33073003; Ficicioglu et al. 2020. PubMed ID: 33202836). Although this variant is not predicted to have a significant impact on splicing according to SpliceAI (score <0.2; Jaganathan et al. 2019. PubMed ID: 30661751), other in silico prediction programs suggest that this variant may weaken the adjacent canonical donor site, leading to exon-skipping and premature protein termination (Alamut Visual Plus v1.6.1). This variant is reported in 0.031% of alleles in individuals of European (Non-Finnish) descent in gnomAD and has conflicting interpretations in ClinVar ranging from likely benign to likely pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/198393/). Of note, it was classified as likely pathogenic by the ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel (VCEP); however, this classification was partially based on internal data not available for independent review. Therefore, although we suspect that this variant may be pathogenic, the clinical significance of this variant is uncertain at this time due to absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	17
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.16
dbscSNV1_RF	Benign	0.41
SpliceAI score (max)		0.17		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs368539333; hg19: chr17-78082409;