rs143713361

Variant names:

• chr10-32336090-C-T
• rs143713361
• NM_001272004.3:c.153+10673G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001272004.3(EPC1):​c.153+10673G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0165 in 137,466 control chromosomes in the GnomAD database, including 32 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 0.017 (32 hom., cov: 28)
• Consequence: EPC1 NM_001272004.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 2 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=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0165 (2271/137466) while in subpopulation NFE AF = 0.0255 (1686/66030). AF 95% confidence interval is 0.0245. There are 32 homozygotes in GnomAd4. There are 1065 alleles in the male GnomAd4 subpopulation. Median coverage is 28. This position passed quality control check.
• BS2: High AC in GnomAd4 at 2271 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPC1	NM_001272004.3	c.153+10673G>A		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.153+10673G>A		intron_variant	Intron 1 of 13	1	NM_001272004.3	ENSP00000318559.6

Frequencies

GnomAD3 genomes AF: 0.0165 AC: 2270 AN: 137402 Hom.: 32 Cov.: 28

Gnomad AFR AF: 0.00497

Gnomad AMI AF: 0.0400

Gnomad AMR AF: 0.00808

Gnomad ASJ AF: 0.0103

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0109

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.0144

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0136

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

GnomAD4 genome AF: 0.0165 AC: 2271 AN: 137466 Hom.: 32 Cov.: 28 AF XY: 0.0160 AC XY: 1065 AN XY: 66422

African (AFR) AF: 0.00496 AC: 165 AN: 33282

American (AMR) AF: 0.00807 AC: 111 AN: 13752

Ashkenazi Jewish (ASJ) AF: 0.0103 AC: 35 AN: 3412

East Asian (EAS) AF: 0.00 AC: 0 AN: 4938

South Asian (SAS) AF: 0.0111 AC: 51 AN: 4590

European-Finnish (FIN) AF: 0.0188 AC: 158 AN: 8400

Middle Eastern (MID) AF: 0.0155 AC: 4 AN: 258

European-Non Finnish (NFE) AF: 0.0255 AC: 1686 AN: 66030

Other (OTH) AF: 0.0135 AC: 26 AN: 1930

Alfa AF: 0.0199 Hom.: 5

Bravo AF: 0.0145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.52
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism

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: rs143713361; hg19: chr10-32625018;