chr17-64521485-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_138363.3(CEP95):c.673C>T(p.Pro225Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000564 in 1,612,790 control chromosomes in the GnomAD database, including 3 homozygotes. 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_138363.3 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 |
---|---|---|---|---|---|---|---|
CEP95 | NM_138363.3 | c.673C>T | p.Pro225Ser | missense_variant | 7/20 | ENST00000556440.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP95 | ENST00000556440.7 | c.673C>T | p.Pro225Ser | missense_variant | 7/20 | 1 | NM_138363.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000559 AC: 85AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000670 AC: 166AN: 247664Hom.: 0 AF XY: 0.000767 AC XY: 103AN XY: 134340
GnomAD4 exome AF: 0.000566 AC: 826AN: 1460514Hom.: 3 Cov.: 29 AF XY: 0.000603 AC XY: 438AN XY: 726532
GnomAD4 genome ? AF: 0.000545 AC: 83AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000604 AC XY: 45AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.673C>T (p.P225S) alteration is located in exon 7 (coding exon 7) of the CEP95 gene. This alteration results from a C to T substitution at nucleotide position 673, causing the proline (P) at amino acid position 225 to be replaced by a serine (S). 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