rs6903252

chr6-145601641-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000638717.1(EPM2A):c.501+33604T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,034 control chromosomes in the GnomAD database, including 20,215 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (20215 hom., cov: 32)
• Consequence: EPM2A ENST00000638717.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

Genes affected

EPM2A (HGNC:3413): (EPM2A glucan phosphatase, laforin) This gene encodes a dual-specificity phosphatase and may be involved in the regulation of glycogen metabolism. The protein acts on complex carbohydrates to prevent glycogen hyperphosphorylation, thus avoiding the formation of insoluble aggregates. Loss-of-function mutations in this gene have been associated with Lafora disease, a rare, adult-onset recessive neurodegenerative disease, which results in myoclonus epilepsy and usually results in death several years after the onset of symptoms. The disease is characterized by the accumulation of insoluble particles called Lafora bodies, which are derived from glycogen. [provided by RefSeq, Jan 2018]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPM2A	XM_011536113.3	c.718+33604T>C		intron_variant
EPM2A	XM_024446550.2	c.718+33604T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPM2A	ENST00000450221.6	c.340+33604T>C		intron_variant		3
EPM2A	ENST00000638717.1	c.501+33604T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76598 AN: 151916 Hom.: 20178 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.487

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.504 AC: 76687 AN: 152034 Hom.: 20215 Cov.: 32 AF XY: 0.506 AC XY: 37592 AN XY: 74314

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.492

Alfa AF: 0.470 Hom.: 7563

Bravo AF: 0.501

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.22
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6903252; hg19: chr6-145922777;