2-24799722-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001322101.2(CENPO):c.94C>T(p.Arg32Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,614,034 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_001322101.2 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 | UniProt |
---|---|---|---|---|---|---|---|
CENPO | NM_001322101.2 | c.94C>T | p.Arg32Cys | missense_variant | 3/8 | ENST00000380834.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPO | ENST00000380834.7 | c.94C>T | p.Arg32Cys | missense_variant | 3/8 | 5 | NM_001322101.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251426Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135880
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461798Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 727198
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2023 | The c.94C>T (p.R32C) alteration is located in exon 3 (coding exon 2) of the CENPO gene. This alteration results from a C to T substitution at nucleotide position 94, causing the arginine (R) at amino acid position 32 to be replaced by a cysteine (C). 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