rs1475435

Variant names:

• chr10-32321615-A-C
• rs1475435
• NM_001272004.3:c.154-15684T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-32321615-A-C
• chr10-32321615-A-G
• chr10-32321615-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001272004.3(EPC1):​c.154-15684T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,576 control chromosomes in the GnomAD database, including 18,601 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 0.45 (18601 hom., cov: 28)
• Consequence: EPC1 NM_001272004.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPC1	NM_001272004.3	c.154-15684T>G		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.154-15684T>G		intron_variant	Intron 1 of 13	1	NM_001272004.3	ENSP00000318559.6

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68264 AN: 151458 Hom.: 18611 Cov.: 28

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.450 AC: 68244 AN: 151576 Hom.: 18601 Cov.: 28 AF XY: 0.453 AC XY: 33515 AN XY: 74038

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.477

Alfa AF: 0.574 Hom.: 35775

Bravo AF: 0.427

Asia WGS AF: 0.575 AC: 2003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
DANN	Benign	0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs1475435; hg19: chr10-32610543;