rs12324931
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001378743.1(CYLD):c.913+1823A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0284 in 152,214 control chromosomes in the GnomAD database, including 108 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 0.028 ( 108 hom., cov: 32)
Consequence
CYLD
NM_001378743.1 intron
NM_001378743.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.89
Genes affected
CYLD (HGNC:2584): (CYLD lysine 63 deubiquitinase) This gene is encodes a cytoplasmic protein with three cytoskeletal-associated protein-glycine-conserved (CAP-GLY) domains that functions as a deubiquitinating enzyme. Mutations in this gene have been associated with cylindromatosis, multiple familial trichoepithelioma, and Brooke-Spiegler syndrome. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
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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=-0.97).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0284 (4322/152214) while in subpopulation NFE AF= 0.0452 (3072/67990). AF 95% confidence interval is 0.0439. There are 108 homozygotes in gnomad4. There are 2005 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 4322 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYLD | NM_001378743.1 | c.913+1823A>C | intron_variant | ENST00000427738.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYLD | ENST00000427738.8 | c.913+1823A>C | intron_variant | 5 | NM_001378743.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0284 AC: 4322AN: 152096Hom.: 108 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0284 AC: 4322AN: 152214Hom.: 108 Cov.: 32 AF XY: 0.0269 AC XY: 2005AN XY: 74416
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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