GeneBe

rs149346325

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001892.6(CSNK1A1):​c.*1098_*1108delTTTTTTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000011 ( 0 hom., cov: 0)

Consequence

CSNK1A1
NM_001892.6 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.54

Publications

0 publications found
Variant links:
Genes affected
CSNK1A1 (HGNC:2451): (casein kinase 1 alpha 1) Enables protein serine/threonine kinase activity. Involved in several processes, including negative regulation of canonical Wnt signaling pathway; peptidyl-serine phosphorylation; and positive regulation of proteasomal ubiquitin-dependent protein catabolic process. Located in centrosome; cytosol; and nuclear speck. Part of beta-catenin destruction complex. Colocalizes with keratin filament and mRNA cleavage and polyadenylation specificity factor complex. Biomarker of Alzheimer's disease and inclusion body myositis. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001892.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CSNK1A1
NM_001892.6
MANE Select
c.*1098_*1108delTTTTTTTTTTT
3_prime_UTR
Exon 10 of 10NP_001883.4
CSNK1A1
NM_001025105.3
c.*1098_*1108delTTTTTTTTTTT
3_prime_UTR
Exon 11 of 11NP_001020276.1P48729-2
CSNK1A1
NM_001271741.2
c.*1098_*1108delTTTTTTTTTTT
3_prime_UTR
Exon 10 of 10NP_001258670.1P48729-3

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CSNK1A1
ENST00000377843.8
TSL:1 MANE Select
c.*1098_*1108delTTTTTTTTTTT
3_prime_UTR
Exon 10 of 10ENSP00000367074.2P48729-1
CSNK1A1
ENST00000261798.10
TSL:1
c.*1098_*1108delTTTTTTTTTTT
3_prime_UTR
Exon 11 of 11ENSP00000261798.6P48729-2
ENSG00000230551
ENST00000499521.2
TSL:1
n.7195_7205delTTTTTTTTTTT
non_coding_transcript_exon
Exon 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.0000108
AC:
1
AN:
92586
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000310
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000108
AC:
1
AN:
92586
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
43022
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
25866
American (AMR)
AF:
0.00
AC:
0
AN:
7812
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2586
East Asian (EAS)
AF:
0.000310
AC:
1
AN:
3228
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2640
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
3340
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
198
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
45086
Other (OTH)
AF:
0.00
AC:
0
AN:
1216
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
2.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs149346325; hg19: chr5-148875307; API