rs8258
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000278935.8(CEP164):c.*792T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,122 control chromosomes in the GnomAD database, including 27,935 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.60 ( 27929 hom., cov: 32)
Exomes 𝑓: 0.67 ( 6 hom. )
Consequence
CEP164
ENST00000278935.8 3_prime_UTR
ENST00000278935.8 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.96
Genes affected
CEP164 (HGNC:29182): (centrosomal protein 164) This gene encodes a centrosomal protein involved in microtubule organization, DNA damage response, and chromosome segregation. The encoded protein is required for assembly of primary cilia and localizes to mature centrioles. Defects in this gene are a cause of nephronophthisis-related ciliopathies. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP164 | NM_014956.5 | c.*792T>C | 3_prime_UTR_variant | 33/33 | ENST00000278935.8 | NP_055771.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP164 | ENST00000278935.8 | c.*792T>C | 3_prime_UTR_variant | 33/33 | 1 | NM_014956.5 | ENSP00000278935 | P1 | ||
CEP164 | ENST00000533706.5 | n.4729T>C | non_coding_transcript_exon_variant | 27/27 | 5 |
Frequencies
GnomAD3 genomes AF: 0.600 AC: 91133AN: 151974Hom.: 27894 Cov.: 32
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GnomAD4 exome AF: 0.667 AC: 20AN: 30Hom.: 6 Cov.: 0 AF XY: 0.700 AC XY: 14AN XY: 20
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GnomAD4 genome AF: 0.600 AC: 91216AN: 152092Hom.: 27929 Cov.: 32 AF XY: 0.594 AC XY: 44148AN XY: 74334
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at