17-80110938-C-G

Position:

• chr17-80110938-C-G

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PP3 PM3 PS3_Moderate PM2_Supporting PP4_Moderate

This summary comes from the ClinGen Evidence Repository: The NM_000152.5:c.1552-3C>G variant in GAA is an intronic variant which occurs within intron 10 and is predicted to impact splicing by disrupting the acceptor splice site (PP3). Experimental studies in fibroblasts from a patient that was homozygous for the variant demonstrated that the variant results in the full inclusion of intron 10, which is predicted to introduce a premature termination codon. However, there was some evidence of normal splicing (PMID 6838077, 25243733) (PS3_Moderate). At least 3 patients with Pompe disease have been reported with this variant including 2 patients with documented GAA deficiency (PP4_Moderate) (PMID 16838077, 28196920, 23430949). Of these patients, one is homozygous for the variant (PMID 16838077) and one is compound heterozygous for the variant and c.-32-13T>G, phase unknown (PMID 16838077) (PM3). The highest population minor allele frequency in gnomAD v2.1.1 is 0.0002713 (35/129024 alleles) in the European (non-Finnish) population, which is lower than the ClinGen LSD VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting). There is a ClinVar entry for this variant (Variation ID: 419722, 2 star review status) with 10 submitters classifying as likely pathogenic or pathogenic and 1 submitter classifying as a variant of uncertain significance. 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 LSD VCEP: PM3, PS3_Moderate, PP4_Moderate, PP3, PM2_Supporting.Classification approved by the ClinGen LSD VCEP on May 16, 2022. LINK:https://erepo.genome.network/evrepo/ui/classification/CA8815383/MONDO:0009290/010

• Frequency:
  • Genomes: 𝑓 0.000079 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00010 (0 hom.)
• Consequence: GAA ENST00000302262.8 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Likely pathogenic reviewed by expert panel P:17
• Conservation: PhyloP100: 0.179

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 8 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: 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/exons	MANE	Protein	UniProt
GAA	NM_000152.5	c.1552-3C>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000302262.8	NP_000143.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAA	ENST00000302262.8	c.1552-3C>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_000152.5	ENSP00000305692	P1

Frequencies

GnomAD3 genomes AF: 0.0000788 AC: 12 AN: 152216 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000135 AC: 34 AN: 251292 Hom.: 0 AF XY: 0.000132 AC XY: 18 AN XY: 135868

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000867

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000273

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000104 AC: 152 AN: 1461624 Hom.: 0 Cov.: 36 AF XY: 0.000105 AC XY: 76 AN XY: 727102

Gnomad4 AFR exome AF: 0.0000597

Gnomad4 AMR exome AF: 0.0000671

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000563

Gnomad4 NFE exome AF: 0.000126

Gnomad4 OTH exome AF: 0.0000662

GnomAD4 genome AF: 0.0000788 AC: 12 AN: 152216 Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4 AN XY: 74358

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000941

Gnomad4 NFE AF: 0.000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000184 Hom.: 0

Bravo AF: 0.000102

EpiCase AF: 0.00

EpiControl AF: 0.000119

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:17

Revision: reviewed by expert panel

Submissions by phenotype

Glycogen storage disease, type II Pathogenic:11

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Nov 06, 2017	Variant summary: The GAA c.1552-3C>G variant involves the alteration of a non-conserved intronic nucleotide and 5/5 splice prediction tools predict an impact on normal splicing. Multiple functional studies support these predictions with findings indicating that the variant does affect splicing (Kroos_2006, Bergsma_2015). This variant was found in 38/277142 control chromosomes, predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.000276 (35/126638), which does not exceed the estimated maximal expected allele frequency of a pathogenic GAA variant (0.0042205). Multiple publications have cited the variant in homozygous affected individuals. In addition, a clinical diagnostic laboratory classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	May 11, 2019	The GAA c.1552-3C>G variant (rs375470378) is reported in the literature in at least one homozygous individual affected with glycogen storage disease II, also called Pompe disease (Bergsma 2015, Kroos 2006). This variant is found in the non-Finnish European population with an overall allele frequency of 0.03% (35/129024 alleles) in the Genome Aggregation Database. This is an intronic variant in a moderately conserved nucleotide, and computational analyses (Alamut v.2.11) predict that this variant impacts splicing by weakening the nearby canonical acceptor splice site. Consistent with these predictions, analyses of patient cDNAs show production of aberrantly spliced mRNAs and reduced mRNA levels compared to those in healthy individuals (Bergsma 2015, Kroos 2006). In addition, fibroblasts from a homozygous individual with this variant exhibited decreased GAA protein levels and substantially reduced GAA enzymatic activity (Bergsma 2015, Kroos 2006). Based on available information, this variant is considered to be likely pathogenic. References: Bergsma AJ et al. Identification and characterization of aberrant GAA pre-mRNA splicing in pompe disease using a generic approach. Hum Mutat. 2015 Jan;36(1):57-68. Kroos M et al. Seven cases of Pompe disease from Greece. J Inherit Metab Dis. 2006 Aug;29(4):556-63. -
Likely pathogenic, reviewed by expert panel	curation	ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	Jun 03, 2022	The NM_000152.5:c.1552-3C>G variant in GAA is an intronic variant which occurs within intron 10 and is predicted to impact splicing by disrupting the acceptor splice site (PP3). Experimental studies in fibroblasts from a patient that was homozygous for the variant demonstrated that the variant results in the full inclusion of intron 10, which is predicted to introduce a premature termination codon. However, there was some evidence of normal splicing (PMID 6838077, 25243733) (PS3_Moderate). At least 3 patients with Pompe disease have been reported with this variant including 2 patients with documented GAA deficiency (PP4_Moderate) (PMID 16838077, 28196920, 23430949). Of these patients, one is homozygous for the variant (PMID 16838077) and one is compound heterozygous for the variant and c.-32-13T>G, phase unknown (PMID 16838077) (PM3). The highest population minor allele frequency in gnomAD v2.1.1 is 0.0002713 (35/129024 alleles) in the European (non-Finnish) population, which is lower than the ClinGen LSD VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting). There is a ClinVar entry for this variant (Variation ID: 419722, 2 star review status) with 10 submitters classifying as likely pathogenic or pathogenic and 1 submitter classifying as a variant of uncertain significance. 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 LSD VCEP: PM3, PS3_Moderate, PP4_Moderate, PP3, PM2_Supporting. Classification approved by the ClinGen LSD VCEP on May 16, 2022. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	This sequence change falls in intron 10 of the GAA gene. It does not directly change the encoded amino acid sequence of the GAA protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs375470378, gnomAD 0.03%). This variant has been observed in individual(s) with glycogen storage disease (PMID: 16838077, 23430949, 25243733, 28196920). ClinVar contains an entry for this variant (Variation ID: 419722). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in multiple aberrant transcripts, the most prominent of which (~80% of total transcript pool) includes all of intron 10 and introduces a premature termination codon (PMID: 16838077, 25243733). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 24, 2024	- -
Likely pathogenic, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 22, 2020	The c.1552-3C>G variant in GAA has been reported in 3 individuals with Glycogen Storage Disease II (PMID: 16838077, 25243733, 28196920) and has also been reported likely pathogenic by Counsyl, Invitae, and EGL Genetic Diagnostics and pathogenic by GeneDx and Integrated Genetics in ClinVar (Variation ID: 419722). This variant has been identified in 0.027% (35/129024) of European (non-Finnish) chromosomes and 0.008% (3/35432) of Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs375470378). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. In vitro functional studies provide some evidence that the c.1552-3C>G variant may cause an impact on splicing in individuals homozygous for this variant with less than 9% of mRNA spliced correctly (PMID: 25243733, 16838077). However, these types of assays may not accurately represent biological function. This variant is located in the 3' splice region. Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein, though some splice predictors do suggest an impact on a splice site. The presence of this variant in the homozygous state and in combination with a reported pathogenic variant, and in individuals with Glycogen Storage Disease II increases the likelihood that the c.1552-3C>G variant is pathogenic (PMID: 28196920, 16838077). The phenotype of individuals homozygous and heterozygous with this variant is highly specific for Glycogen Storage Disease II with abnormally low GAA activity detected in their leukocytes and the absence of known pseudodeficiency alleles in one individual (PMID: 28196920, 16838077). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic. ACMG/AMP Criteria applied: PP4_Moderate, PM3, PM2, PS3_Supporting (Richards 2015). -
Pathogenic, criteria provided, single submitter	clinical testing	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Jan 09, 2019	This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PM2,PP3. -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Mar 17, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Nov 08, 2021	NM_000152.3(GAA):c.1552-3C>G is an intronic variant classified as likely pathogenic in the context of Pompe disease. c.1552-3C>G has been observed in cases with relevant disease (PMID: 28196920, 16838077, 23430949, 33202836). Functional assessments of this variant are available in the literature (PMID: 16838077, 25243733, 27623443). c.1552-3C>G has been observed in population frequency databases (gnomAD: NFE 0.03%). In summary, NM_000152.3(GAA):c.1552-3C>G is an intronic variant that has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
Pathogenic, criteria provided, single submitter	curation	Laboratory of Medical Genetics, National & Kapodistrian University of Athens	Feb 01, 2024	- -

not provided Pathogenic:5

Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Mar 28, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2023	GAA: PM2, PM3, PP3, PS3:Supporting -
Likely pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Sep 16, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 01, 2015	The c.1552-3 C>G variant has been previously reported as a homozygous variant in a patient with a mild form of GSDII (Kroos et al., 2006). Functional studies demonstrate that the c.1552-3 C>G variantcauses aberrant gene splicing and results in reduced enzyme activity (Kroos et al., 2006; Bergsma et al., 2015). It was not observed with any significant frequency in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project.Therefore, we interpret c.1552-3 C>G as a pathogenic variant. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Mar 16, 2017	- -

Cardiovascular phenotype Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 17, 2023

The c.1552-3C>G intronic variant results from a C to G substitution 3 nucleotides upstream from coding exon 10 in the GAA gene. This alteration has been reported as homozygous and compound heterozygous in individuals with Pompe disease, including those with low enzyme activity (Kroos M et al. J Inherit Metab Dis, 2006 Aug;29:556-63; Wittmann J et al. JIMD Rep, 2012 Mar;6:117-25; Lin N et al. Clin Chem, 2017 Apr;63:842-851; Ficicioglu C et al. Int J Neonatal Screen, 2020 Nov;6:[ePub ahead of print]). Additionally, aberrant splicing was observed in an in vitro study (Kroos M et al. J Inherit Metab Dis, 2006 Aug;29:556-63). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and may result in the creation or strengthening of a novel splice acceptor site. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.92

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.95
SpliceAI score (max)		0.87		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.34		Position offset: -27
DS_AL_spliceai		0.87		Position offset: 3

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

Publications

LitVar

Other links and lift over

dbSNP: rs375470378; hg19: chr17-78084737;