rs368539333

chr17-80108610-G-Cchr17-80108610-G-T

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PM2 PP5_Very_Strong BP4

The NM_000152.5(GAA):c.1194+3G>C variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000246 in 1,612,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★★).

• Frequency:
  • Genomes: 𝑓 0.000072 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00026 (0 hom.)
• Consequence: GAA NM_000152.5 splice_donor_region, intron
• Scores: Splicing: ADA: 0.1642
• Clinical Significance: Likely pathogenic reviewed by expert panel P:4 U:8 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 Likely_pathogenic. Variant got 9 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 17-80108610-G-C is Pathogenic according to our data. Variant chr17-80108610-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 198393.Status of the report is reviewed_by_expert_panel, 3 stars.
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAA	NM_000152.5	c.1194+3G>C		splice_donor_region_variant, intron_variant		ENST00000302262.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAA	ENST00000302262.8	c.1194+3G>C		splice_donor_region_variant, intron_variant		1	NM_000152.5	P1

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: Likely pathogenic

Submissions summary: Pathogenic:4 Uncertain:8 Benign:1

Revision: reviewed by expert panel

Submissions by phenotype

Glycogen storage disease, type II Pathogenic:3 Uncertain:3

Likely pathogenic, reviewed by expert panel	curation	ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	Dec 06, 2022	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 three patients, all with documented laboratory values showing deficient GAA activity (Clinical Diagnostic Laboratories, PMID: 33073003) (PP4_Moderate). All of these patients are compound heterozygous for the variant and another variant in GAA that has been classified as pathogenic or likely pathogenic by the ClinGen LSD VCEP, including c.1781G>A (p.Arg594His), LP (mother is heterozygous for c.1781G>A, no paternal testing), (Clinical Laboratory, PMID: 33073003); c.1210G>A (p.Asp404Asn), confirmed in trans (Clinical Laboratory), and c.1841C>A (p.Thr614Lys), phase unknown,(Clinical Laboratory (PM3_Strong). The computational predictor SpliceAI does not predict a strong impact on splicing (all scores<0.2). However, varSEAK classifies that variant as having a splicing effect (class 5). There is a ClinVar entry for this variant (Variation ID: 198393). In summary, this variant meets the criteria to be classified as likely pathogenic for Pompe disease. GAA-specific ACMG-AMP criteria met, as specified by the ClinGen Lysosomal Storage Disorders VCEP (Specifications Version 2.0): PM3_Strong, PP4_Moderate, PM2_Supporting. (Classification approved by the ClinGen LSD VCEP on December 6, 2022) -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Sep 05, 2021	- -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Jan 24, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Aug 17, 2023	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 07, 2024	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; Invitae; External communication). 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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 07, 2023	- -

not provided Pathogenic:1 Uncertain:4 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jan 12, 2023	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 (Ficicioglu C et al., 2020; Burton BK et al., 2020); In silico analysis supports that this variant does not alter splicing; This variant is associated with the following publications: (PMID: 33073003, 33202836) -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 22, 2015	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Oct 19, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2024	GAA: BP4 -
Uncertain significance, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Mar 22, 2023

Variant summary: GAA c.1194+3G>C alters a 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 a 5' splicing donor site. Three predict the variant weakens a 5' donor site. Three predict the variant creates a 3' acceptor site. 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 reported in the literature during newborn screening in patients with low GAA activity and second pathogenic variants (Burton_2019, Ficicioglu_2020). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Seven ClinVar submitters have classified the variant: six submitters have classified the variant as VUS while an expert panel has classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

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;