rs141321114
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001813.3(CENPE):c.7886G>A(p.Arg2629Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000323 in 1,613,828 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001813.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPE | NM_001813.3 | c.7886G>A | p.Arg2629Gln | missense_variant | 48/49 | ENST00000265148.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPE | ENST00000265148.9 | c.7886G>A | p.Arg2629Gln | missense_variant | 48/49 | 2 | NM_001813.3 | A2 | |
CENPE | ENST00000380026.8 | c.7523G>A | p.Arg2508Gln | missense_variant | 46/47 | 1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000289 AC: 44AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000577 AC: 145AN: 251232Hom.: 0 AF XY: 0.000641 AC XY: 87AN XY: 135776
GnomAD4 exome AF: 0.000328 AC: 479AN: 1461624Hom.: 3 Cov.: 31 AF XY: 0.000382 AC XY: 278AN XY: 727124
GnomAD4 genome ? AF: 0.000276 AC: 42AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 05, 2017 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | CENPE: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at