rs10242197

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001287135.2(CDK14):​c.123+26349C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,026 control chromosomes in the GnomAD database, including 2,608 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 0.18 ( 2608 hom., cov: 32)

Consequence

CDK14
NM_001287135.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310
Variant links:
Genes affected
CDK14 (HGNC:8883): (cyclin dependent kinase 14) Enables cyclin binding activity and cyclin-dependent protein serine/threonine kinase activity. Involved in G2/M transition of mitotic cell cycle and regulation of canonical Wnt signaling pathway. Located in cytosol; nucleoplasm; and plasma membrane. Part of cytoplasmic cyclin-dependent protein kinase holoenzyme complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CDK14NM_001287135.2 linkuse as main transcriptc.123+26349C>T intron_variant ENST00000380050.8 NP_001274064.1 O94921-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDK14ENST00000380050.8 linkuse as main transcriptc.123+26349C>T intron_variant 1 NM_001287135.2 ENSP00000369390.3 O94921-1

Frequencies

GnomAD3 genomes
AF:
0.181
AC:
27444
AN:
151908
Hom.:
2599
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.164
Gnomad AMI
AF:
0.319
Gnomad AMR
AF:
0.145
Gnomad ASJ
AF:
0.191
Gnomad EAS
AF:
0.0337
Gnomad SAS
AF:
0.194
Gnomad FIN
AF:
0.222
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.200
Gnomad OTH
AF:
0.188
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.181
AC:
27485
AN:
152026
Hom.:
2608
Cov.:
32
AF XY:
0.181
AC XY:
13440
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.165
Gnomad4 AMR
AF:
0.144
Gnomad4 ASJ
AF:
0.191
Gnomad4 EAS
AF:
0.0337
Gnomad4 SAS
AF:
0.193
Gnomad4 FIN
AF:
0.222
Gnomad4 NFE
AF:
0.200
Gnomad4 OTH
AF:
0.193
Alfa
AF:
0.197
Hom.:
1723
Bravo
AF:
0.173
Asia WGS
AF:
0.161
AC:
560
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.3
DANN
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10242197; hg19: chr7-90259912; API