rs2593068
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_025009.5(CEP135):c.700-958G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,998 control chromosomes in the GnomAD database, including 23,864 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 0.55 ( 23864 hom., cov: 33)
Consequence
CEP135
NM_025009.5 intron
NM_025009.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0800
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 Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP135 | NM_025009.5 | c.700-958G>A | intron_variant | ENST00000257287.5 | NP_079285.2 | |||
CEP135 | XM_006714055.4 | c.700-958G>A | intron_variant | XP_006714118.1 | ||||
LOC124900705 | XR_007058124.1 | n.197+7457C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP135 | ENST00000257287.5 | c.700-958G>A | intron_variant | 1 | NM_025009.5 | ENSP00000257287.3 | ||||
CEP135 | ENST00000515081.1 | n.334-958G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.554 AC: 84140AN: 151880Hom.: 23810 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.554 AC: 84243AN: 151998Hom.: 23864 Cov.: 33 AF XY: 0.557 AC XY: 41357AN XY: 74252
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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