16-58167069-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001896.4(CSNK2A2):c.726+138G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 574,318 control chromosomes in the GnomAD database, including 8,392 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.14 ( 2026 hom., cov: 32)
Exomes 𝑓: 0.17 ( 6366 hom. )
Consequence
CSNK2A2
NM_001896.4 intron
NM_001896.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.125
Genes affected
CSNK2A2 (HGNC:2459): (casein kinase 2 alpha 2) This gene encodes the alpha', or alpha 2, catalytic subunit of the protein kinase enzyme, casein kinase 2 (CK2). Casein kinase 2 is a serine/threonine protein kinase that phosphorylates acidic proteins such as casein. It is involved in various cellular processes, including cell cycle control, apoptosis, and circadian rhythms. This heterotetrameric kinase includes two catalytic subunits, either alpha or alpha', and two regulatory beta subunits. The closely related gene paralog encoding the alpha, or alpha 1 subunit (CSNK2A1, Gene ID: 1457) is found on chromosome 20. An intronic variant in this gene (alpha 2) may be associated with leukocyte telomere length in a South Asian population. A related transcribed pseudogene is found on chromosome 11. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 16-58167069-C-T is Benign according to our data. Variant chr16-58167069-C-T is described in ClinVar as [Benign]. Clinvar id is 1264105.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSNK2A2 | NM_001896.4 | c.726+138G>A | intron_variant | ENST00000262506.8 | NP_001887.1 | |||
CSNK2A2 | XM_047433626.1 | c.726+138G>A | intron_variant | XP_047289582.1 | ||||
CSNK2A2 | XM_017022945.2 | c.402+138G>A | intron_variant | XP_016878434.1 | ||||
CSNK2A2 | XM_005255801.4 | c.315+138G>A | intron_variant | XP_005255858.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSNK2A2 | ENST00000262506.8 | c.726+138G>A | intron_variant | 1 | NM_001896.4 | ENSP00000262506.3 |
Frequencies
GnomAD3 genomes AF: 0.142 AC: 21608AN: 152022Hom.: 2021 Cov.: 32
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GnomAD4 exome AF: 0.167 AC: 70424AN: 422178Hom.: 6366 AF XY: 0.164 AC XY: 35797AN XY: 218386
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GnomAD4 genome AF: 0.142 AC: 21627AN: 152140Hom.: 2026 Cov.: 32 AF XY: 0.149 AC XY: 11088AN XY: 74358
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at