chr1-26242051-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001319944.2(CEP85):c.56-2115T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,198 control chromosomes in the GnomAD database, including 22,463 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 0.53 ( 22463 hom., cov: 31)
Consequence
CEP85
NM_001319944.2 intron
NM_001319944.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.72
Genes affected
CEP85 (HGNC:25309): (centrosomal protein 85) This gene encodes a protein that belongs to the centrosome-associated family of proteins. The centrosome is a subcellular organelle in the animal cell that functions as a microtubule organizing center and is involved in cell-cycle progression. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP85 | NM_001319944.2 | c.56-2115T>C | intron_variant | ENST00000451429.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP85 | ENST00000451429.8 | c.56-2115T>C | intron_variant | 2 | NM_001319944.2 | A1 | |||
CEP85 | ENST00000252992.8 | c.56-2115T>C | intron_variant | 1 | P4 | ||||
CEP85 | ENST00000640292.2 | c.55+2213T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.531 AC: 80254AN: 151076Hom.: 22457 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.531 AC: 80290AN: 151198Hom.: 22463 Cov.: 31 AF XY: 0.520 AC XY: 38442AN XY: 73876
GnomAD4 genome
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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