2-65069601-T-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015147.3(CEP68):āc.157T>Gā(p.Ser53Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,840 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015147.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP68 | NM_015147.3 | c.157T>G | p.Ser53Ala | missense_variant | 2/7 | ENST00000377990.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP68 | ENST00000377990.7 | c.157T>G | p.Ser53Ala | missense_variant | 2/7 | 1 | NM_015147.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 250696Hom.: 2 AF XY: 0.0000959 AC XY: 13AN XY: 135586
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461702Hom.: 2 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 727156
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2022 | The c.157T>G (p.S53A) alteration is located in exon 2 (coding exon 1) of the CEP68 gene. This alteration results from a T to G substitution at nucleotide position 157, causing the serine (S) at amino acid position 53 to be replaced by an alanine (A). 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