7-90819060-G-A

Variant summary

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

The NM_001287135.2(CDK14):​c.544+28408G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,794 control chromosomes in the GnomAD database, including 15,195 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 0.44 ( 15195 hom., cov: 31)

Consequence

CDK14
NM_001287135.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.476
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]

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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=-0.63).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CDK14NM_001287135.2 linkuse as main transcriptc.544+28408G>A intron_variant ENST00000380050.8 NP_001274064.1
CDK14NM_001287136.1 linkuse as main transcriptc.406+28408G>A intron_variant NP_001274065.1
CDK14NM_001287137.1 linkuse as main transcriptc.157+28408G>A intron_variant NP_001274066.1
CDK14NM_012395.3 linkuse as main transcriptc.490+28408G>A intron_variant NP_036527.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDK14ENST00000380050.8 linkuse as main transcriptc.544+28408G>A intron_variant 1 NM_001287135.2 ENSP00000369390 P4O94921-1

Frequencies

GnomAD3 genomes
AF:
0.436
AC:
66079
AN:
151678
Hom.:
15194
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.445
Gnomad AMI
AF:
0.293
Gnomad AMR
AF:
0.525
Gnomad ASJ
AF:
0.398
Gnomad EAS
AF:
0.817
Gnomad SAS
AF:
0.448
Gnomad FIN
AF:
0.473
Gnomad MID
AF:
0.354
Gnomad NFE
AF:
0.379
Gnomad OTH
AF:
0.427
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.435
AC:
66102
AN:
151794
Hom.:
15195
Cov.:
31
AF XY:
0.442
AC XY:
32813
AN XY:
74156
show subpopulations
Gnomad4 AFR
AF:
0.444
Gnomad4 AMR
AF:
0.526
Gnomad4 ASJ
AF:
0.398
Gnomad4 EAS
AF:
0.817
Gnomad4 SAS
AF:
0.449
Gnomad4 FIN
AF:
0.473
Gnomad4 NFE
AF:
0.379
Gnomad4 OTH
AF:
0.423
Alfa
AF:
0.397
Hom.:
5800
Bravo
AF:
0.442
Asia WGS
AF:
0.591
AC:
2050
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.63
CADD
Benign
13
DANN
Benign
0.61

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs3824039; hg19: chr7-90448375; API