rs2069454
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004935.4(CDK5):c.313-47G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.046 in 1,325,908 control chromosomes in the GnomAD database, including 1,541 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 0.047 ( 227 hom., cov: 32)
Exomes 𝑓: 0.046 ( 1314 hom. )
Consequence
CDK5
NM_004935.4 intron
NM_004935.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.179
Genes affected
CDK5 (HGNC:1774): (cyclin dependent kinase 5) This gene encodes a proline-directed serine/threonine kinase that is a member of the cyclin-dependent kinase family of proteins. Unlike other members of the family, the protein encoded by this gene does not directly control cell cycle regulation. Instead the protein, which is predominantly expressed at high levels in mammalian postmitotic central nervous system neurons, functions in diverse processes such as synaptic plasticity and neuronal migration through phosphorylation of proteins required for cytoskeletal organization, endocytosis and exocytosis, and apoptosis. In humans, an allelic variant of the gene that results in undetectable levels of the protein has been associated with lethal autosomal recessive lissencephaly-7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2015]
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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=-0.8).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0651 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDK5 | NM_004935.4 | c.313-47G>C | intron_variant | ENST00000485972.6 | |||
CDK5 | NM_001164410.3 | c.313-289G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDK5 | ENST00000485972.6 | c.313-47G>C | intron_variant | 1 | NM_004935.4 | P1 | |||
CDK5 | ENST00000297518.4 | c.313-289G>C | intron_variant | 1 | |||||
CDK5 | ENST00000476691.1 | n.466G>C | non_coding_transcript_exon_variant | 1/2 | 4 | ||||
CDK5 | ENST00000487703.5 | n.677-47G>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0474 AC: 7217AN: 152184Hom.: 229 Cov.: 32
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GnomAD3 exomes AF: 0.0406 AC: 7201AN: 177296Hom.: 180 AF XY: 0.0422 AC XY: 3985AN XY: 94372
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GnomAD4 exome AF: 0.0458 AC: 53778AN: 1173606Hom.: 1314 Cov.: 16 AF XY: 0.0463 AC XY: 27334AN XY: 590730
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GnomAD4 genome ? AF: 0.0474 AC: 7224AN: 152302Hom.: 227 Cov.: 32 AF XY: 0.0466 AC XY: 3469AN XY: 74470
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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