chr10-32326517-A-G

Variant names:

• chr10-32326517-A-G
• rs11599044
• NM_001272004.3:c.153+20246T>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+20246T>C 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 152,160 control chromosomes in the GnomAD database, including 2,042 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 (2042 hom., cov: 31)
• Consequence: EPC1 NM_025209.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 6 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=-0.81).
• 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+20246T>C		intron	N/A	NP_001258933.1
	EPC1	NM_025209.5		c.153+20246T>C		intron	N/A	NP_079485.1
	EPC1	NM_001382753.1		c.153+20246T>C		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+20246T>C		intron	N/A	ENSP00000318559.6
	EPC1	ENST00000263062.8	TSL:1	c.153+20246T>C		intron	N/A	ENSP00000263062.8
	EPC1	ENST00000375110.6	TSL:1	c.4-20586T>C		intron	N/A	ENSP00000364251.2

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22916 AN: 152042 Hom.: 2031 Cov.: 31

Gnomad AFR AF: 0.0758

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.0742

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.151 AC: 22937 AN: 152160 Hom.: 2042 Cov.: 31 AF XY: 0.157 AC XY: 11684 AN XY: 74374

African (AFR) AF: 0.0756 AC: 3140 AN: 41518

American (AMR) AF: 0.221 AC: 3383 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0742 AC: 257 AN: 3464

East Asian (EAS) AF: 0.238 AC: 1230 AN: 5170

South Asian (SAS) AF: 0.325 AC: 1568 AN: 4820

European-Finnish (FIN) AF: 0.164 AC: 1744 AN: 10602

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

European-Non Finnish (NFE) AF: 0.165 AC: 11251 AN: 67992

Other (OTH) AF: 0.134 AC: 284 AN: 2112

Alfa AF: 0.150 Hom.: 316

Bravo AF: 0.145

Asia WGS AF: 0.274 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.80
PhyloP100		-0.43
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: rs11599044; hg19: chr10-32615445;