chr4-103123040-G-C

Position:

chr4-103123040-G-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001813.3(CENPE):c.6974C>G(p.Ser2325Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00673 in 1,613,702 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0055 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0069 ( 79 hom. )

Consequence

CENPE
NM_001813.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.103

Variant links:

Genes affected

CENPE (HGNC:1856): (centromere protein E) Centrosome-associated protein E (CENPE) is a kinesin-like motor protein that accumulates in the G2 phase of the cell cycle. Unlike other centrosome-associated proteins, it is not present during interphase and first appears at the centromere region of chromosomes during prometaphase. This protein is required for stable spindle microtubule capture at kinetochores which is a necessary step in chromosome alignment during prometaphase. This protein also couples chromosome position to microtubule depolymerizing activity. Alternative splicing results in multiple transcript variants encoding distinct protein isoforms. [provided by RefSeq, Nov 2014]

CENPE links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0037833452).

BP6

Variant 4-103123040-G-C is Benign according to our data. Variant chr4-103123040-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 376761.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00553 (841/152174) while in subpopulation SAS AF= 0.0185 (89/4810). AF 95% confidence interval is 0.0154. There are 4 homozygotes in gnomad4. There are 399 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CENPE	NM_001813.3 linkuse as main transcript	c.6974C>G	p.Ser2325Cys	missense_variant	43/49	ENST00000265148.9	NP_001804.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CENPE	ENST00000265148.9 linkuse as main transcript	c.6974C>G	p.Ser2325Cys	missense_variant	43/49	2	NM_001813.3	ENSP00000265148	A2	Q02224-1
CENPE	ENST00000380026.8 linkuse as main transcript	c.6611C>G	p.Ser2204Cys	missense_variant	41/47	1		ENSP00000369365	P2	Q02224-3

Frequencies

GnomAD3 genomes

AF:

0.00553

AC:

841

AN:

152058

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00111

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00550

Gnomad ASJ

AF:

0.0245

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0183

Gnomad FIN

AF:

0.000566

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00743

Gnomad OTH

AF:

0.0100

GnomAD3 exomes

AF:

0.00712

AC:

1788

AN:

251248

Hom.:

AF XY:

0.00846

AC XY:

1149

AN XY:

135790

show subpopulations

Gnomad AFR exome

AF:

0.000738

Gnomad AMR exome

AF:

0.00295

Gnomad ASJ exome

AF:

0.0189

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0207

Gnomad FIN exome

AF:

0.000508

Gnomad NFE exome

AF:

0.00691

Gnomad OTH exome

AF:

0.00882

GnomAD4 exome

AF:

0.00686

AC:

10022

AN:

1461528

Hom.:

Cov.:

AF XY:

0.00749

AC XY:

5446

AN XY:

727086

show subpopulations

Gnomad4 AFR exome

AF:

0.00108

Gnomad4 AMR exome

AF:

0.00302

Gnomad4 ASJ exome

AF:

0.0191

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0205

Gnomad4 FIN exome

AF:

0.000674

Gnomad4 NFE exome

AF:

0.00627

Gnomad4 OTH exome

AF:

0.00803

GnomAD4 genome

AF:

0.00553

AC:

841

AN:

152174

Hom.:

Cov.:

AF XY:

0.00536

AC XY:

399

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.00111

Gnomad4 AMR

AF:

0.00550

Gnomad4 ASJ

AF:

0.0245

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0185

Gnomad4 FIN

AF:

0.000566

Gnomad4 NFE

AF:

0.00743

Gnomad4 OTH

AF:

0.00947

Alfa

AF:

0.00732

Hom.:

Bravo

AF:

0.00505

TwinsUK

AF:

0.00674

AC:

ALSPAC

AF:

0.00752

AC:

ESP6500AA

AF:

0.00113

AC:

ESP6500EA

AF:

0.00744

AC:

ExAC

AF:

0.00713

AC:

865

Asia WGS

AF:

0.00664

AC:

AN:

3478

EpiCase

AF:

0.00736

EpiControl

AF:

0.00771

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Feb 13, 2017	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 21, 2019	- -

CENPE-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 18, 2019

This variant is classified as 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

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.51

CADD

Benign

8.8

DANN

Benign

0.97

DEOGEN2

Benign

0.030

T;.;.

Eigen

Benign

-0.92

Eigen_PC

Benign

-0.87

FATHMM_MKL

Benign

0.011

LIST_S2

Benign

0.59

T;T;T

MetaRNN

Benign

0.0038

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.060

N;.;.

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.34

PROVEAN

Benign

2.5

N;N;.

REVEL

Benign

0.066

Sift

Benign

0.29

T;T;.

Sift4G

Benign

0.23

T;T;T

Polyphen

0.0

B;B;.

Vest4

0.21

MVP

0.28

MPC

0.038

ClinPred

0.0025

GERP RS

1.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.035

gMVP

0.11

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over