NM_001272004.3:c.1391+780G>A

Variant names:

• chr10-32285914-C-T
• rs11008865
• NM_001272004.3:c.1391+780G>A

Variant summary

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

The NM_001272004.3(EPC1):​c.1391+780G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,922 control chromosomes in the GnomAD database, including 2,136 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 0.16 (2136 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: EPC1 NM_001272004.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

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 = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPC1	NM_001272004.3	c.1391+780G>A		intron_variant	Intron 9 of 13	ENST00000319778.11	NP_001258933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPC1	ENST00000319778.11	c.1391+780G>A		intron_variant	Intron 9 of 13	1	NM_001272004.3	ENSP00000318559.6

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23842 AN: 151804 Hom.: 2124 Cov.: 32

Gnomad AFR AF: 0.0983

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.141

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.157 AC: 23878 AN: 151922 Hom.: 2136 Cov.: 32 AF XY: 0.163 AC XY: 12129 AN XY: 74226

Gnomad4 AFR AF: 0.0985

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.0741

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.139

Alfa AF: 0.158 Hom.: 1724

Bravo AF: 0.152

Asia WGS AF: 0.278 AC: 964 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
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: rs11008865; hg19: chr10-32574842;