NM_015630.4:c.154-9572G>A

Variant names:

• chr2-148680642-G-A
• rs6759083
• NM_015630.4:c.154-9572G>A

Variant summary

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

The NM_015630.4(EPC2):​c.154-9572G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,062 control chromosomes in the GnomAD database, including 4,931 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 0.24 (4931 hom., cov: 32)
• Consequence: EPC2 NM_015630.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 10 publications found

Genes affected

EPC2 (HGNC:24543): (enhancer of polycomb homolog 2) Predicted to contribute to histone acetyltransferase activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be part of Piccolo NuA4 histone acetyltransferase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPC2	NM_015630.4	c.154-9572G>A		intron_variant	Intron 1 of 13	ENST00000258484.11	NP_056445.3
EPC2	XM_011510941.3	c.154-9572G>A		intron_variant	Intron 1 of 13		XP_011509243.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPC2	ENST00000258484.11	c.154-9572G>A		intron_variant	Intron 1 of 13	1	NM_015630.4	ENSP00000258484.6
EPC2	ENST00000457184.6	c.82-9572G>A		intron_variant	Intron 2 of 14	5		ENSP00000415543.2
EPC2	ENST00000397424.2	c.-60-9572G>A		intron_variant	Intron 1 of 4	3		ENSP00000380569.2
EPC2	ENST00000409654.5	c.154-9572G>A		intron_variant	Intron 1 of 2	3		ENSP00000387097.1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35953 AN: 151944 Hom.: 4917 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.237 AC: 35994 AN: 152062 Hom.: 4931 Cov.: 32 AF XY: 0.245 AC XY: 18228 AN XY: 74318

African (AFR) AF: 0.183 AC: 7614 AN: 41506

American (AMR) AF: 0.347 AC: 5293 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3470

East Asian (EAS) AF: 0.510 AC: 2637 AN: 5168

South Asian (SAS) AF: 0.409 AC: 1973 AN: 4822

European-Finnish (FIN) AF: 0.270 AC: 2848 AN: 10538

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13915 AN: 67980

Other (OTH) AF: 0.255 AC: 537 AN: 2108

Alfa AF: 0.222 Hom.: 2355

Bravo AF: 0.242

Asia WGS AF: 0.449 AC: 1560 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.48
PhyloP100		0.21
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: rs6759083; hg19: chr2-149438211;