Genetic Variant EPPK1:p.Thr2308Thr (chr8-143866330-G-A) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_031308.4(EPPK1):c.6924C>T(p.Thr2308Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000024 ( 0 hom., cov: 6)

Exomes 𝑓: 0.000015 ( 0 hom. )

Consequence

EPPK1
NM_031308.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -5.76

Variant links:

Genes affected

EPPK1 (HGNC:15577): (epiplakin 1) The protein encoded by this gene belongs to the plakin family of proteins, which play a role in the organization of cytoskeletal architecture. This family member is composed of several highly homologous plakin repeats. It may function to maintain the integrity of keratin intermediate filament networks in epithelial cells. Studies of the orthologous mouse protein suggest that it accelerates keratinocyte migration during wound healing. [provided by RefSeq, Oct 2013]

EPPK1 links:

ENSG00000305900 (HGNC:):

ENSG00000305900 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 8-143866330-G-A is Benign according to our data. Variant chr8-143866330-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3030626.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-5.76 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPPK1	NM_031308.4 link	c.6924C>T	p.Thr2308Thr	synonymous_variant	Exon 2 of 2	ENST00000615648.2	NP_112598.3	P58107

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
EPPK1	ENST00000615648.2 link	c.6924C>T	p.Thr2308Thr	synonymous_variant	Exon 2 of 2	5	NM_031308.4	ENSP00000484472.1	P58107
EPPK1	ENST00000568225.2 link	c.6849C>T	p.Thr2283Thr	synonymous_variant	Exon 1 of 1	6		ENSP00000456124.2	A0A075B730
ENSG00000305900	ENST00000813856.1 link	n.157+12757C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0000240

AC:

AN:

41610

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000107

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00

AC:

AN:

249158

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000151

AC:

AN:

397410

Hom.:

Cov.:

AF XY:

0.00000976

AC XY:

AN XY:

204912

show subpopulations

African (AFR)

AF:

0.000274

AC:

AN:

10958

American (AMR)

AF:

0.00

AC:

AN:

12642

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11690

East Asian (EAS)

AF:

0.00

AC:

AN:

27012

South Asian (SAS)

AF:

0.00

AC:

AN:

25468

European-Finnish (FIN)

AF:

0.00

AC:

AN:

24988

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1716

European-Non Finnish (NFE)

AF:

0.00000769

AC:

AN:

260044

Other (OTH)

AF:

0.0000437

AC:

AN:

22892

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000240

AC:

AN:

41610

Hom.:

Cov.:

AF XY:

0.0000513

AC XY:

AN XY:

19502

show subpopulations

African (AFR)

AF:

0.000107

AC:

AN:

9370

American (AMR)

AF:

0.00

AC:

AN:

4572

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1126

East Asian (EAS)

AF:

0.00

AC:

AN:

1836

South Asian (SAS)

AF:

0.00

AC:

AN:

1446

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3296

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

19238

Other (OTH)

AF:

0.00

AC:

AN:

490

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

EPPK1-related disorder

Benign:1

Apr 28, 2021

PreventionGenetics, part of Exact Sciences

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

(source)

DANN

Benign

0.95

PhyloP100

-5.8

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

Below is the list of publications found by LitVar for variant 8:143866330 G>A . It may be empty.

chr8-143866330-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over