Genetic Variant CSNK1A1:c.*1108dupT (chr5-149495744-T-TA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001892.6(CSNK1A1):c.*1108dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.37 ( 4614 hom., cov: 0)

Exomes 𝑓: 0.083 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

CSNK1A1
NM_001892.6 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.157

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]

CSNK1A1 links:

ENSG00000230551 (HGNC:):

ENSG00000230551 links:

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new If you want to explore the variant's impact on the transcript NM_001892.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CSNK1A1	NM_001892.6	MANE Select	c.*1108dupT	3_prime_UTR	Exon 10 of 10	NP_001883.4
CSNK1A1	NM_001025105.3		c.*1108dupT	3_prime_UTR	Exon 11 of 11	NP_001020276.1	P48729-2
CSNK1A1	NM_001271741.2		c.*1108dupT	3_prime_UTR	Exon 10 of 10	NP_001258670.1	P48729-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CSNK1A1	ENST00000377843.8	TSL:1 MANE Select	c.*1108dupT	3_prime_UTR	Exon 10 of 10	ENSP00000367074.2	P48729-1
CSNK1A1	ENST00000261798.10	TSL:1	c.*1108dupT	3_prime_UTR	Exon 11 of 11	ENSP00000261798.6	P48729-2
ENSG00000230551	ENST00000499521.2	TSL:1	n.7205dupT	non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.375

AC:

34709

AN:

92522

Hom.:

4618

Cov.:

show subpopulations

Gnomad AFR

AF:

0.409

Gnomad AMI

AF:

0.400

Gnomad AMR

AF:

0.336

Gnomad ASJ

AF:

0.437

Gnomad EAS

AF:

0.337

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.284

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.400

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0833

AC:

AN:

192

Hom.:

Cov.:

AF XY:

0.0948

AC XY:

AN XY:

116

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0842

AC:

AN:

190

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.564

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.375

AC:

34687

AN:

92502

Hom.:

4614

Cov.:

AF XY:

0.368

AC XY:

15817

AN XY:

42982

show subpopulations

African (AFR)

AF:

0.409

AC:

10566

AN:

25838

American (AMR)

AF:

0.336

AC:

2625

AN:

7822

Ashkenazi Jewish (ASJ)

AF:

0.437

AC:

1133

AN:

2594

East Asian (EAS)

AF:

0.336

AC:

1080

AN:

3212

South Asian (SAS)

AF:

0.251

AC:

658

AN:

2620

European-Finnish (FIN)

AF:

0.284

AC:

947

AN:

3338

Middle Eastern (MID)

AF:

0.375

AC:

AN:

176

European-Non Finnish (NFE)

AF:

0.375

AC:

16883

AN:

45074

Other (OTH)

AF:

0.398

AC:

484

AN:

1216

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

1110

2219

3329

4438

5548

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

348

696

1044

1392

1740

<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.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.16

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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5-149495744-TAAAAAAAAAAA-TAAAAAAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over