rs1553288629
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000366955.8(CENPF):āc.1816A>Gā(p.Lys606Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000209 in 1,432,722 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
ENST00000366955.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CENPF | NM_016343.4 | c.1816A>G | p.Lys606Glu | missense_variant | 12/20 | ENST00000366955.8 | NP_057427.3 | |
CENPF | XM_017000086.3 | c.1816A>G | p.Lys606Glu | missense_variant | 12/20 | XP_016855575.1 | ||
CENPF | XM_011509082.4 | c.1816A>G | p.Lys606Glu | missense_variant | 12/19 | XP_011507384.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CENPF | ENST00000366955.8 | c.1816A>G | p.Lys606Glu | missense_variant | 12/20 | 1 | NM_016343.4 | ENSP00000355922 | P2 | |
CENPF | ENST00000706765.1 | c.1816A>G | p.Lys606Glu | missense_variant | 12/19 | ENSP00000516538 | A2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000209 AC: 3AN: 1432722Hom.: 0 Cov.: 33 AF XY: 0.00000281 AC XY: 2AN XY: 712182
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 27, 2017 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 08, 2023 | The c.1816A>G (p.K606E) alteration is located in exon 12 (coding exon 11) of the CENPF gene. This alteration results from a A to G substitution at nucleotide position 1816, causing the lysine (K) at amino acid position 606 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at