rs11592754

chr10-32330644-A-Cchr10-32330644-A-T

Variant summary

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

The NM_001272004.3(EPC1):c.153+16119T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,222 control chromosomes in the GnomAD database, including 1,347 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 0.11 (1347 hom., cov: 32)
• Consequence: EPC1 NM_001272004.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPC1	NM_001272004.3	c.153+16119T>G		intron_variant		ENST00000319778.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPC1	ENST00000319778.11	c.153+16119T>G		intron_variant		1	NM_001272004.3	P1

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17421 AN: 152102 Hom.: 1339 Cov.: 32

Gnomad AFR AF: 0.0260

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.115 AC: 17435 AN: 152222 Hom.: 1347 Cov.: 32 AF XY: 0.120 AC XY: 8941 AN XY: 74434

Gnomad4 AFR AF: 0.0259

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.105

Alfa AF: 0.130 Hom.: 1486

Bravo AF: 0.108

Asia WGS AF: 0.189 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.6
Dann	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs11592754; hg19: chr10-32619572;