rs141352776
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016343.4(CENPF):c.4171G>A(p.Glu1391Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000205 in 1,611,414 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000092 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
CENPF
NM_016343.4 missense
NM_016343.4 missense
Scores
3
3
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.91
Genes affected
CENPF (HGNC:1857): (centromere protein F) This gene encodes a protein that associates with the centromere-kinetochore complex. The protein is a component of the nuclear matrix during the G2 phase of interphase. In late G2 the protein associates with the kinetochore and maintains this association through early anaphase. It localizes to the spindle midzone and the intracellular bridge in late anaphase and telophase, respectively, and is thought to be subsequently degraded. The localization of this protein suggests that it may play a role in chromosome segregation during mitotis. It is thought to form either a homodimer or heterodimer. Autoantibodies against this protein have been found in patients with cancer or graft versus host disease. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPF | NM_016343.4 | c.4171G>A | p.Glu1391Lys | missense_variant | 12/20 | ENST00000366955.8 | |
CENPF | XM_017000086.3 | c.4171G>A | p.Glu1391Lys | missense_variant | 12/20 | ||
CENPF | XM_011509082.4 | c.4171G>A | p.Glu1391Lys | missense_variant | 12/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPF | ENST00000366955.8 | c.4171G>A | p.Glu1391Lys | missense_variant | 12/20 | 1 | NM_016343.4 | P2 | |
CENPF | ENST00000706765.1 | c.4171G>A | p.Glu1391Lys | missense_variant | 12/19 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152172Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000363 AC: 9AN: 247930Hom.: 0 AF XY: 0.0000373 AC XY: 5AN XY: 133994
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GnomAD4 exome AF: 0.0000130 AC: 19AN: 1459242Hom.: 0 Cov.: 35 AF XY: 0.0000110 AC XY: 8AN XY: 725636
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GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74334
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at