rs11594963

Variant names:

• chr10-32336808-G-A
• rs11594963
• NM_001272004.3:c.153+9955C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-32336808-G-A
• chr10-32336808-G-C

Variant summary

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

The NM_025209.5(EPC1):​c.153+9955C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,196 control chromosomes in the GnomAD database, including 2,100 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 (2100 hom., cov: 32)
• Consequence: EPC1 NM_025209.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025209.5. 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.153+9955C>T		intron	N/A	NP_001258933.1
	EPC1	NM_025209.5		c.153+9955C>T		intron	N/A	NP_079485.1
	EPC1	NM_001382753.1		c.153+9955C>T		intron	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.153+9955C>T		intron	N/A	ENSP00000318559.6
	EPC1	ENST00000263062.8	TSL:1	c.153+9955C>T		intron	N/A	ENSP00000263062.8
	EPC1	ENST00000375110.6	TSL:1	c.4-30877C>T		intron	N/A	ENSP00000364251.2

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23504 AN: 152076 Hom.: 2089 Cov.: 32

Gnomad AFR AF: 0.0900

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.155 AC: 23535 AN: 152196 Hom.: 2100 Cov.: 32 AF XY: 0.161 AC XY: 11977 AN XY: 74400

African (AFR) AF: 0.0900 AC: 3741 AN: 41544

American (AMR) AF: 0.223 AC: 3406 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1232 AN: 5168

South Asian (SAS) AF: 0.326 AC: 1571 AN: 4826

European-Finnish (FIN) AF: 0.165 AC: 1742 AN: 10568

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11213 AN: 68014

Other (OTH) AF: 0.138 AC: 292 AN: 2110

Alfa AF: 0.148 Hom.: 473

Bravo AF: 0.149

Asia WGS AF: 0.279 AC: 965 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.4
DANN	Benign	0.63
PhyloP100		2.3
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: rs11594963; hg19: chr10-32625736;