Variant rs2306001 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_017957.3(EPN3):c.563-111G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0895 in 900,114 control chromosomes in the GnomAD database, including 4,303 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 0.070 ( 498 hom., cov: 33)

Exomes 𝑓: 0.094 ( 3805 hom. )

Consequence

EPN3
NM_017957.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.28

Variant links:

Genes affected

EPN3 (HGNC:18235): (epsin 3) Predicted to enable clathrin binding activity and phospholipid binding activity. Predicted to be involved in endocytosis. Located in clathrin-coated vesicle; nucleoplasm; and perinuclear region of cytoplasm. Is extrinsic component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

EPN3 links:

(HGNC:):

links:

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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPN3	NM_017957.3 linkuse as main transcript	c.563-111G>A		intron_variant		ENST00000268933.8
LOC105371824	NR_135675.1 linkuse as main transcript	n.358C>T		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPN3	ENST00000268933.8 linkuse as main transcript	c.563-111G>A		intron_variant		2	NM_017957.3	P1	Q9H201-1
	ENST00000654456.1 linkuse as main transcript	n.441C>T		non_coding_transcript_exon_variant	2/3

Frequencies

GnomAD3 genomes

AF:

0.0698

AC:

10630

AN:

152206

Hom.:

499

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0193

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.0431

Gnomad ASJ

AF:

0.0429

Gnomad EAS

AF:

0.0212

Gnomad SAS

AF:

0.0492

Gnomad FIN

AF:

0.0914

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.111

Gnomad OTH

AF:

0.0554

GnomAD4 exome

AF:

0.0936

AC:

69969

AN:

747790

Hom.:

3805

Cov.:

AF XY:

0.0923

AC XY:

35858

AN XY:

388360

show subpopulations

Gnomad4 AFR exome

AF:

0.0175

Gnomad4 AMR exome

AF:

0.0326

Gnomad4 ASJ exome

AF:

0.0423

Gnomad4 EAS exome

AF:

0.0291

Gnomad4 SAS exome

AF:

0.0531

Gnomad4 FIN exome

AF:

0.0961

Gnomad4 NFE exome

AF:

0.113

Gnomad4 OTH exome

AF:

0.0809

GnomAD4 genome

AF:

0.0697

AC:

10624

AN:

152324

Hom.:

498

Cov.:

AF XY:

0.0685

AC XY:

5099

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0192

Gnomad4 AMR

AF:

0.0429

Gnomad4 ASJ

AF:

0.0429

Gnomad4 EAS

AF:

0.0214

Gnomad4 SAS

AF:

0.0491

Gnomad4 FIN

AF:

0.0914

Gnomad4 NFE

AF:

0.111

Gnomad4 OTH

AF:

0.0543

Alfa

AF:

0.0952

Hom.:

228

Bravo

AF:

0.0642

Asia WGS

AF:

0.0320

AC:

113

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.8

DANN

Benign

0.75

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over