chr2-24815604-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001322101.2(CENPO):c.442C>T(p.Leu148Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,614,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001322101.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPO | NM_001322101.2 | c.442C>T | p.Leu148Phe | missense_variant | 5/8 | ENST00000380834.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPO | ENST00000380834.7 | c.442C>T | p.Leu148Phe | missense_variant | 5/8 | 5 | NM_001322101.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000219 AC: 55AN: 251488Hom.: 0 AF XY: 0.000265 AC XY: 36AN XY: 135916
GnomAD4 exome AF: 0.000134 AC: 196AN: 1461806Hom.: 0 Cov.: 32 AF XY: 0.000140 AC XY: 102AN XY: 727206
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 09, 2021 | The c.442C>T (p.L148F) alteration is located in exon 5 (coding exon 4) of the CENPO gene. This alteration results from a C to T substitution at nucleotide position 442, causing the leucine (L) at amino acid position 148 to be replaced by a phenylalanine (F). 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