chr4-103109050-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.Lys2588Lys) 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
Consequence
NM_001813.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CENPE | ENST00000265148.9 | c.7764G>A | p.Lys2588Lys | synonymous_variant | Exon 48 of 49 | 2 | NM_001813.3 | ENSP00000265148.3 | ||
CENPE | ENST00000380026.8 | c.7401G>A | p.Lys2467Lys | synonymous_variant | Exon 46 of 47 | 1 | ENSP00000369365.3 |
Frequencies
GnomAD3 genomes AF: 0.0101 AC: 1538AN: 152052Hom.: 32 Cov.: 32
GnomAD3 exomes AF: 0.00268 AC: 670AN: 250194Hom.: 10 AF XY: 0.00195 AC XY: 264AN XY: 135306
GnomAD4 exome AF: 0.000969 AC: 1415AN: 1460836Hom.: 20 Cov.: 31 AF XY: 0.000808 AC XY: 587AN XY: 726708
GnomAD4 genome AF: 0.0102 AC: 1547AN: 152170Hom.: 31 Cov.: 32 AF XY: 0.00979 AC XY: 728AN XY: 74386
ClinVar
Submissions by phenotype
not provided Benign:3
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CENPE-related disorder Benign:1
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at