10-32346904-CAG-TAA

Variant names:

• chr10-32346904-CAG-TAA
• NM_001272004.3:c.10_12delCTGinsTTA
• EPC1 p.5

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The NM_001272004.3(EPC1):​c.10_12delCTGinsTTA​(p.5) variant causes a synonymous change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: EPC1 NM_001272004.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 8.04
• Publications: 0 publications found

Genes affected

EPC1 (HGNC:19876): (enhancer of polycomb homolog 1) This gene encodes a member of the polycomb group (PcG) family. The encoded protein is a component of the NuA4 histone acetyltransferase complex and can act as both a transcriptional activator and repressor. The encoded protein has been linked to apoptosis, DNA repair, skeletal muscle differentiation, gene silencing, and adult T-cell leukemia/lymphoma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

EPC1-AS2 (HGNC:56646): (EPC1 antisense RNA 2)

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001272004.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPC1	NM_001272004.3	MANE Select	c.10_12delCTGinsTTA	p.5	synonymous	N/A	NP_001258933.1	Q9H2F5-2
	EPC1	NM_025209.5		c.10_12delCTGinsTTA	p.5	synonymous	N/A	NP_079485.1	Q9H2F5-1
	EPC1	NM_001382753.1		c.10_12delCTGinsTTA	p.5	synonymous	N/A	NP_001369682.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPC1	ENST00000319778.11	TSL:1 MANE Select	c.10_12delCTGinsTTA	p.5	synonymous	N/A	ENSP00000318559.6	Q9H2F5-2
	EPC1	ENST00000263062.8	TSL:1	c.10_12delCTGinsTTA	p.5	synonymous	N/A	ENSP00000263062.8	Q9H2F5-1
	EPC1	ENST00000375110.6	TSL:1	c.3+31585_3+31587delCTGinsTTA		intron	N/A	ENSP00000364251.2	Q9H2F5-3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		8.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr10-32635832;