4-103109050-C-T
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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
NM_001813.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.804
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 |
---|---|---|---|---|---|---|---|---|
CENPE | NM_001813.3 | c.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 |
---|---|---|---|---|---|---|---|---|---|---|
CENPE | ENST00000265148.9 | c.7764G>A | p.Lys2588= | synonymous_variant | 48/49 | 2 | NM_001813.3 | ENSP00000265148 | A2 | |
CENPE | ENST00000380026.8 | c.7401G>A | p.Lys2467= | synonymous_variant | 46/47 | 1 | ENSP00000369365 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0101 AC: 1538AN: 152052Hom.: 32 Cov.: 32
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GnomAD3 exomes AF: 0.00268 AC: 670AN: 250194Hom.: 10 AF XY: 0.00195 AC XY: 264AN XY: 135306
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GnomAD4 exome AF: 0.000969 AC: 1415AN: 1460836Hom.: 20 Cov.: 31 AF XY: 0.000808 AC XY: 587AN XY: 726708
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GnomAD4 genome AF: 0.0102 AC: 1547AN: 152170Hom.: 31 Cov.: 32 AF XY: 0.00979 AC XY: 728AN XY: 74386
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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 submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 01, 2021 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
CENPE-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 15, 2024 | 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at