2-24799719-T-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001322101.2(CENPO):c.91T>A(p.Ser31Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000284 in 1,613,914 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPO | NM_001322101.2 | c.91T>A | p.Ser31Thr | missense_variant | 3/8 | ENST00000380834.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPO | ENST00000380834.7 | c.91T>A | p.Ser31Thr | missense_variant | 3/8 | 5 | NM_001322101.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000251 AC: 63AN: 251380Hom.: 0 AF XY: 0.000309 AC XY: 42AN XY: 135848
GnomAD4 exome AF: 0.000292 AC: 427AN: 1461792Hom.: 2 Cov.: 30 AF XY: 0.000308 AC XY: 224AN XY: 727196
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2022 | The c.91T>A (p.S31T) alteration is located in exon 3 (coding exon 2) of the CENPO gene. This alteration results from a T to A substitution at nucleotide position 91, causing the serine (S) at amino acid position 31 to be replaced by a threonine (T). 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