chr15-48738244-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_001194998.2(CEP152):c.*5G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000183 in 1,610,128 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 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP152 | ENST00000380950 | c.*5G>A | 3_prime_UTR_variant | Exon 27 of 27 | 1 | NM_001194998.2 | ENSP00000370337.2 | |||
CEP152 | ENST00000399334 | c.*5G>A | 3_prime_UTR_variant | Exon 26 of 26 | 1 | ENSP00000382271.3 | ||||
CEP152 | ENST00000561245.1 | n.142+3387G>A | intron_variant | Intron 2 of 3 | 2 | ENSP00000453591.1 |
Frequencies
GnomAD3 genomes AF: 0.000848 AC: 129AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000212 AC: 52AN: 245060Hom.: 0 AF XY: 0.000218 AC XY: 29AN XY: 133002
GnomAD4 exome AF: 0.000114 AC: 166AN: 1457912Hom.: 0 Cov.: 31 AF XY: 0.0000993 AC XY: 72AN XY: 724804
GnomAD4 genome AF: 0.000847 AC: 129AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.000739 AC XY: 55AN XY: 74432
ClinVar
Submissions by phenotype
Microcephaly 9, primary, autosomal recessive Uncertain:1
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not provided Uncertain:1
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CEP152-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at