4-103109050-C-T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_001813.3(CENPE):​c.7764G>A​(p.Lys2588=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00184 in 1,613,006 control chromosomes in the GnomAD database, including 51 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.010 ( 31 hom., cov: 32)
Exomes 𝑓: 0.00097 ( 20 hom. )

Consequence

CENPE
NM_001813.3 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.804
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.27).
BP6
Variant 4-103109050-C-T is Benign according to our data. Variant chr4-103109050-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 786043.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.804 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0102 (1547/152170) while in subpopulation AFR AF= 0.035 (1455/41524). AF 95% confidence interval is 0.0335. There are 31 homozygotes in gnomad4. There are 728 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 31 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CENPENM_001813.3 linkuse as main transcriptc.7764G>A p.Lys2588= synonymous_variant 48/49 ENST00000265148.9 NP_001804.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CENPEENST00000265148.9 linkuse as main transcriptc.7764G>A p.Lys2588= synonymous_variant 48/492 NM_001813.3 ENSP00000265148 A2Q02224-1
CENPEENST00000380026.8 linkuse as main transcriptc.7401G>A p.Lys2467= synonymous_variant 46/471 ENSP00000369365 P2Q02224-3

Frequencies

GnomAD3 genomes
AF:
0.0101
AC:
1538
AN:
152052
Hom.:
32
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0349
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00472
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.0000944
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000735
Gnomad OTH
AF:
0.00576
GnomAD3 exomes
AF:
0.00268
AC:
670
AN:
250194
Hom.:
10
AF XY:
0.00195
AC XY:
264
AN XY:
135306
show subpopulations
Gnomad AFR exome
AF:
0.0378
Gnomad AMR exome
AF:
0.00145
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000989
Gnomad FIN exome
AF:
0.0000926
Gnomad NFE exome
AF:
0.0000529
Gnomad OTH exome
AF:
0.000494
GnomAD4 exome
AF:
0.000969
AC:
1415
AN:
1460836
Hom.:
20
Cov.:
31
AF XY:
0.000808
AC XY:
587
AN XY:
726708
show subpopulations
Gnomad4 AFR exome
AF:
0.0343
Gnomad4 AMR exome
AF:
0.00204
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000139
Gnomad4 FIN exome
AF:
0.0000749
Gnomad4 NFE exome
AF:
0.0000162
Gnomad4 OTH exome
AF:
0.00227
GnomAD4 genome
AF:
0.0102
AC:
1547
AN:
152170
Hom.:
31
Cov.:
32
AF XY:
0.00979
AC XY:
728
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.0350
Gnomad4 AMR
AF:
0.00471
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.0000944
Gnomad4 NFE
AF:
0.0000735
Gnomad4 OTH
AF:
0.00570
Alfa
AF:
0.00537
Hom.:
8
Bravo
AF:
0.0114
Asia WGS
AF:
0.00260
AC:
10
AN:
3476
EpiCase
AF:
0.00
EpiControl
AF:
0.000178

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 31, 2019- -
Likely benign, criteria provided, single submitterclinical testingGeneDxMar 01, 2021- -
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
CENPE-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesApr 15, 2024This 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
BayesDel_noAF
Benign
-0.27
CADD
Benign
6.6
DANN
Benign
0.59

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. It may be empty.

Other links and lift over

dbSNP: rs61758372; hg19: chr4-104030207; API