rs2370759

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001272004.3(EPC1):​c.153+719C>T 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 151,868 control chromosomes in the GnomAD database, including 2,040 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 ( 2040 hom., cov: 32)

Consequence

EPC1
NM_001272004.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.255
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EPC1NM_001272004.3 linkuse as main transcriptc.153+719C>T intron_variant ENST00000319778.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EPC1ENST00000319778.11 linkuse as main transcriptc.153+719C>T intron_variant 1 NM_001272004.3 P1Q9H2F5-2

Frequencies

GnomAD3 genomes
AF:
0.151
AC:
22866
AN:
151750
Hom.:
2031
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0763
Gnomad AMI
AF:
0.0527
Gnomad AMR
AF:
0.220
Gnomad ASJ
AF:
0.0738
Gnomad EAS
AF:
0.238
Gnomad SAS
AF:
0.326
Gnomad FIN
AF:
0.165
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.165
Gnomad OTH
AF:
0.136
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.151
AC:
22885
AN:
151868
Hom.:
2040
Cov.:
32
AF XY:
0.157
AC XY:
11678
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.0761
Gnomad4 AMR
AF:
0.221
Gnomad4 ASJ
AF:
0.0738
Gnomad4 EAS
AF:
0.239
Gnomad4 SAS
AF:
0.328
Gnomad4 FIN
AF:
0.165
Gnomad4 NFE
AF:
0.165
Gnomad4 OTH
AF:
0.134
Alfa
AF:
0.156
Hom.:
2431
Bravo
AF:
0.144
Asia WGS
AF:
0.274
AC:
948
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
3.7
DANN
Benign
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2370759; hg19: chr10-32634972; API