10-32326207-T-C

Variant names:

• chr10-32326207-T-C
• rs16933243
• NM_001272004.3:c.154-20276A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001272004.3(EPC1):​c.154-20276A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,102 control chromosomes in the GnomAD database, including 2,052 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 0.15 (2052 hom., cov: 32)
• Consequence: EPC1 NM_001272004.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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.154-20276A>G		intron_variant	Intron 1 of 13	ENST00000319778.11	NP_001258933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPC1	ENST00000319778.11	c.154-20276A>G		intron_variant	Intron 1 of 13	1	NM_001272004.3	ENSP00000318559.6

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22999 AN: 151982 Hom.: 2040 Cov.: 32

Gnomad AFR AF: 0.0776

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.151 AC: 23028 AN: 152102 Hom.: 2052 Cov.: 32 AF XY: 0.158 AC XY: 11745 AN XY: 74350

African (AFR) AF: 0.0777 AC: 3223 AN: 41502

American (AMR) AF: 0.222 AC: 3385 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3468

East Asian (EAS) AF: 0.238 AC: 1232 AN: 5170

South Asian (SAS) AF: 0.327 AC: 1575 AN: 4822

European-Finnish (FIN) AF: 0.164 AC: 1740 AN: 10578

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11249 AN: 67968

Other (OTH) AF: 0.136 AC: 287 AN: 2112

Alfa AF: 0.142 Hom.: 204

Bravo AF: 0.145

Asia WGS AF: 0.278 AC: 962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.52
PhyloP100		-0.75
Mutation Taster		=100/0	polymorphism (auto)

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: rs16933243; hg19: chr10-32615135;