rs3814098

Positions:

• chr7-91209554-G-C
• chr7-91209554-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001287135.2(CDK14):​c.*2418G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 152,502 control chromosomes in the GnomAD database, including 62,565 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 0.91 (62368 hom., cov: 30)
  • Exomes 𝑓: 0.94 (197 hom.)
• Consequence: CDK14 NM_001287135.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.58

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.*2418G>C		3_prime_UTR_variant	15/15	ENST00000380050.8	NP_001274064.1
CDK14	NM_012395.3	c.*2418G>C		3_prime_UTR_variant	14/14		NP_036527.1
CDK14	NM_001287136.1	c.*2418G>C		3_prime_UTR_variant	14/14		NP_001274065.1
CDK14	NM_001287137.1	c.*2418G>C		3_prime_UTR_variant	13/13		NP_001274066.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000380050.8	c.*2418G>C		3_prime_UTR_variant	15/15	1	NM_001287135.2	ENSP00000369390.3
CDK14	ENST00000265741.7	c.*2418G>C		3_prime_UTR_variant	14/14	1		ENSP00000265741.3
CDK14	ENST00000406263.5	c.*2418G>C		3_prime_UTR_variant	14/14	1		ENSP00000385034.1
CDK14	ENST00000436577.3	c.*2418G>C		3_prime_UTR_variant	13/13	2		ENSP00000398936.2

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137537 AN: 151948 Hom.: 62319 Cov.: 30

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.903

GnomAD4 exome AF: 0.945 AC: 412 AN: 436 Hom.: 197 Cov.: 0 AF XY: 0.943 AC XY: 247 AN XY: 262

Gnomad4 FIN exome AF: 0.949

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.905 AC: 137639 AN: 152066 Hom.: 62368 Cov.: 30 AF XY: 0.908 AC XY: 67515 AN XY: 74316

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.867

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.936

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.898

Alfa AF: 0.899 Hom.: 2929

Bravo AF: 0.904

Asia WGS AF: 0.902 AC: 3135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	15
DANN	Benign	0.66

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

Other links and lift over

dbSNP: rs3814098; hg19: chr7-90838869;