rs786204561

chr17-80118359-T-A

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1_Moderate PM2 PP3_Strong PP5_Very_Strong

The NM_000152.5(GAA):c.2646+2T>A variant causes a splice donor change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: GAA NM_000152.5 splice_donor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Likely pathogenic reviewed by expert panel P:5
• Conservation: PhyloP100: 5.35

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 Pathogenic. Variant got 16 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.028681356 fraction of the gene. Cryptic splice site detected, with MaxEntScore 4.8, offset of 25, new splice context is: ctgGTgggc. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 17-80118359-T-A is Pathogenic according to our data. Variant chr17-80118359-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 188924.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-80118359-T-A is described in Lovd as [Pathogenic]. Variant chr17-80118359-T-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAA	NM_000152.5	c.2646+2T>A		splice_donor_variant		ENST00000302262.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAA	ENST00000302262.8	c.2646+2T>A		splice_donor_variant		1	NM_000152.5	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:5

Revision: reviewed by expert panel

Submissions by phenotype

Glycogen storage disease, type II Pathogenic:4

Likely pathogenic, criteria provided, single submitter	literature only	Counsyl	Aug 21, 2014	- -
Likely pathogenic, reviewed by expert panel	curation	ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	Apr 20, 2020	This variant, c.2646+2T>A, alters the canonical donor splice site of intron 18. RT-PCR analysis revealed that the variant results in the use of a cryptic splice site in exon 18, deleting the last 21 nucleotides of the exon, corresponding to the loss of 7 amino acids (PMID 11854868). As <10% of the protein in lost, PVS1_Moderate was applied. The variant is not in gnomAD v2.1.1, meeting PM2. Four individuals with this variant have been reported to have Pompe disease and residual GAA activity meeting the ClinGen LSD VCEP's specifications for PP4. These individuals are compound heterozygous for the variant and another pathogenic variant in GAA, either an 8 kb deletion extending from intron 7 to intron 15 (PMID 11854868; in trans, 1 point), c.2481+102_2646+31del (PMID 17616415; phase unknown), c.573C>A (p.Tyr191Ter) (PMID 11738358; phase unknown), and c.1942G>A (p.Gly648Ser) (PMID 29422078; note that in trans data from this patient will be used in the classification of p.Gly648Ser and is not included here in order to avoid a circular argument). This in trans data meets PM3_Strong. Another patient has been reported but was not included because the residual GAA activity was not provided and therefore PP4 cannot be assessed (PMID 28380188). There is a ClinVar entry for this variant (Variation ID: 188924, 1 star status) with one submitter classifying the variant as likely pathogenic. In summary, this variant meets the criteria to be classified as likely pathogenic for Pompe disease. GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen LSD VCEP: PVS1_Moderate, PM2, PM3_Strong, PP4. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 13, 2021	Variant summary: GAA c.2646+2T>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5 splicing donor site. Experimental evidence supports these predictions demonstrating that the variant results in use of a cryptic splice site in exon 18 leading to deletion of the terminal 21 nucleotides of exon 18 (Huie_2002). The variant was absent in 207926 control chromosomes (gnomAD). c.2646+2T>A has been reported in the literature in multiple compound heterozygous individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease) (examples: Fernandez-Hojas_2002, Huie_2002, Gort_2007, Bevilacqua_2020, and Viamonte_2021). These data indicate that the variant is very likely to be associated with disease. Two ClinVar submitters including an expert panel (ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel) (evaluation after 2014) cite the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Nov 06, 2023	This sequence change affects a donor splice site in intron 18 of the GAA gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in GAA are known to be pathogenic (PMID: 18425781, 22252923). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with Pompe disease (PMID: 11738358, 29422078). ClinVar contains an entry for this variant (Variation ID: 188924). 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. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Revvity Omics, Revvity

Oct 08, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Uncertain	0.080
Cadd	Pathogenic	34
Dann	Uncertain	0.98
Eigen	Pathogenic	0.98
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Pathogenic	1.0	D
MutationTaster	Benign	1.0	D;D
GERP RS		5.7

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.89
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.87		Position offset: -23
DS_DL_spliceai		1.0		Position offset: -2

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

Publications

LitVar

Other links and lift over

dbSNP: rs786204561; hg19: chr17-78092158;