4-55955640-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000257287.5(CEP135):c.472+1257C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,096 control chromosomes in the GnomAD database, including 1,536 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 0.13 ( 1536 hom., cov: 32)
Consequence
CEP135
ENST00000257287.5 intron
ENST00000257287.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.252
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP135 | NM_025009.5 | c.472+1257C>T | intron_variant | ENST00000257287.5 | NP_079285.2 | |||
LOC124900705 | XR_007058124.1 | n.198-3169G>A | intron_variant, non_coding_transcript_variant | |||||
CEP135 | XM_006714055.4 | c.472+1257C>T | intron_variant | XP_006714118.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP135 | ENST00000257287.5 | c.472+1257C>T | intron_variant | 1 | NM_025009.5 | ENSP00000257287 | P1 | |||
CEP135 | ENST00000422247.6 | c.472+1257C>T | intron_variant | 2 | ENSP00000412799 | |||||
CEP135 | ENST00000515081.1 | n.106+1257C>T | intron_variant, non_coding_transcript_variant | 2 | ||||||
CEP135 | ENST00000706800.1 | n.645+1257C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.127 AC: 19275AN: 151978Hom.: 1530 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.127 AC: 19298AN: 152096Hom.: 1536 Cov.: 32 AF XY: 0.131 AC XY: 9720AN XY: 74344
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ClinVar
Not reported inComputational scores
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Name
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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