chr6-145735475-C-A

Variant names:

• chr6-145735475-C-A
• rs587780938
• NM_005670.4:c.24G>T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_005670.4(EPM2A):​c.24G>T​(p.Val8Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000377 in 1,061,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. V8V) has been classified as Benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000038 (0 hom.)
• Consequence: EPM2A NM_005670.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369
• Publications: 0 publications found

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]

ENSG00000288551 (HGNC:):

EPM2A-DT (HGNC:48990): (EPM2A divergent transcript)

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BP7: Synonymous conserved (PhyloP=0.369 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005670.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPM2A	NM_005670.4	MANE Select	c.24G>T	p.Val8Val	synonymous	Exon 1 of 4	NP_005661.1
	EPM2A	NM_001360071.2		c.-646G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 5	NP_001347000.1
	EPM2A	NM_001368131.1		c.-344G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 4	NP_001355060.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPM2A	ENST00000367519.9	TSL:1 MANE Select	c.24G>T	p.Val8Val	synonymous	Exon 1 of 4	ENSP00000356489.3
	EPM2A	ENST00000435470.2	TSL:1	c.24G>T	p.Val8Val	synonymous	Exon 1 of 5	ENSP00000405913.2
	EPM2A	ENST00000638262.1	TSL:1	c.24G>T	p.Val8Val	synonymous	Exon 1 of 3	ENSP00000492876.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000377 AC: 4 AN: 1061220 Hom.: 0 Cov.: 34 AF XY: 0.00000395 AC XY: 2 AN XY: 506852

African (AFR) AF: 0.00 AC: 0 AN: 21406

American (AMR) AF: 0.00 AC: 0 AN: 8364

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12746

East Asian (EAS) AF: 0.00 AC: 0 AN: 22432

South Asian (SAS) AF: 0.00 AC: 0 AN: 24194

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 19962

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2744

European-Non Finnish (NFE) AF: 0.00000440 AC: 4 AN: 908284

Other (OTH) AF: 0.00 AC: 0 AN: 41088

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	11
DANN	Benign	0.91
PhyloP100		0.37
PromoterAI		-0.0097	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs587780938; hg19: chr6-146056611;