7-91209554-G-C

Variant names:

• chr7-91209554-G-C
• rs3814098
• NM_001287135.2:c.*2418G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001287135.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK14	NM_001287135.2	MANE Select	c.*2418G>C		3_prime_UTR	Exon 15 of 15	NP_001274064.1
	CDK14	NM_012395.3		c.*2418G>C		3_prime_UTR	Exon 14 of 14	NP_036527.1
	CDK14	NM_001287136.1		c.*2418G>C		3_prime_UTR	Exon 14 of 14	NP_001274065.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK14	ENST00000380050.8	TSL:1 MANE Select	c.*2418G>C		3_prime_UTR	Exon 15 of 15	ENSP00000369390.3
	CDK14	ENST00000265741.7	TSL:1	c.*2418G>C		3_prime_UTR	Exon 14 of 14	ENSP00000265741.3
	CDK14	ENST00000406263.5	TSL:1	c.*2418G>C		3_prime_UTR	Exon 14 of 14	ENSP00000385034.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.949 AC: 406 AN: 428

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 0.500 AC: 2 AN: 4

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

African (AFR) AF: 0.936 AC: 38816 AN: 41482

American (AMR) AF: 0.909 AC: 13892 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3003 AN: 3464

East Asian (EAS) AF: 0.885 AC: 4565 AN: 5158

South Asian (SAS) AF: 0.936 AC: 4511 AN: 4820

European-Finnish (FIN) AF: 0.931 AC: 9835 AN: 10566

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59975 AN: 67980

Other (OTH) AF: 0.898 AC: 1897 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	15
DANN	Benign	0.66
PhyloP100		2.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3814098; hg19: chr7-90838869;