4-55991942-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_025009.5(CEP135):c.1866C>T(p.Ser622=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000824 in 1,456,890 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000084 ( 0 hom. )
Consequence
CEP135
NM_025009.5 synonymous
NM_025009.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.695
Genes affected
CEP135 (HGNC:29086): (centrosomal protein 135) This gene encodes a centrosomal protein, which acts as a scaffolding protein during early centriole biogenesis, and is also required for centriole-centriole cohesion during interphase. Mutations in this gene are associated with autosomal recessive primary microcephaly-8. [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP7
Synonymous conserved (PhyloP=-0.695 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| CEP135 | NM_025009.5 | c.1866C>T | p.Ser622= | synonymous_variant | 15/26 | ENST00000257287.5 | |
| CEP135 | XM_006714055.4 | c.1833C>T | p.Ser611= | synonymous_variant | 15/26 | ||
| CEP135 | XM_005265788.5 | c.795C>T | p.Ser265= | synonymous_variant | 8/19 | ||
| CEP135 | XM_011534412.2 | c.336C>T | p.Ser112= | synonymous_variant | 5/16 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CEP135 | ENST00000257287.5 | c.1866C>T | p.Ser622= | synonymous_variant | 15/26 | 1 | NM_025009.5 | P1 | |
| CEP135 | ENST00000506202.1 | n.1816C>T | non_coding_transcript_exon_variant | 8/19 | 1 |
Frequencies
GnomAD3 genomes 0.00000660 AC: 1AN: 151408Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000104 AC: 2AN: 192638Hom.: 0 AF XY: 0.00000943 AC XY: 1AN XY: 106066
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GnomAD4 exome AF: 0.00000843 AC: 11AN: 1305482Hom.: 0 Cov.: 25 AF XY: 0.0000107 AC XY: 7AN XY: 652952
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GnomAD4 genome 0.00000660 AC: 1AN: 151408Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73858
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at