15-48738251-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_001194998.2(CEP152):c.5131T>A(p.Ter1711Lysext*?) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000164 in 1,459,480 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001194998.2 stop_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP152 | ENST00000380950.7 | c.5131T>A | p.Ter1711Lysext*? | stop_lost | Exon 27 of 27 | 1 | NM_001194998.2 | ENSP00000370337.2 | ||
CEP152 | ENST00000399334.7 | c.4963T>A | p.Ter1655Lysext*? | stop_lost | Exon 26 of 26 | 1 | ENSP00000382271.3 | |||
CEP152 | ENST00000561245.1 | n.142+3380T>A | intron_variant | Intron 2 of 3 | 2 | ENSP00000453591.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 246960Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 133994
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1459480Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 725746
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
CEP152-related disorder Uncertain:1
The CEP152 c.4963T>A (p.Ter1655LysextTer6) variant is a stop-lost variant. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of stop-lost variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for CEP152-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at