rs17862241

Variant names:

• chr7-90592034-G-A
• rs17862241
• ENST00000430760.5:c.-93-12184G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000430760.5(CDK14):​c.-93-12184G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,934 control chromosomes in the GnomAD database, including 15,929 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 0.45 (15929 hom., cov: 32)
  • Exomes 𝑓: 0.38 (0 hom.)
• Consequence: CDK14 ENST00000430760.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 4 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]

ENSG00000223969 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000430760.5	c.-93-12184G>A		intron_variant	Intron 1 of 5	1		ENSP00000394570.1
CDK14	ENST00000449528.5	c.-47-12184G>A		intron_variant	Intron 4 of 7	1		ENSP00000393616.1
CDK14	ENST00000456689.5	c.-148-12184G>A		intron_variant	Intron 1 of 6	1		ENSP00000406848.1

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68149 AN: 151808 Hom.: 15926 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.387

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.436

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

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: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.449 AC: 68169 AN: 151926 Hom.: 15929 Cov.: 32 AF XY: 0.447 AC XY: 33206 AN XY: 74264

African (AFR) AF: 0.344 AC: 14262 AN: 41436

American (AMR) AF: 0.379 AC: 5789 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1641 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1750 AN: 5166

South Asian (SAS) AF: 0.469 AC: 2257 AN: 4812

European-Finnish (FIN) AF: 0.551 AC: 5804 AN: 10540

Middle Eastern (MID) AF: 0.382 AC: 110 AN: 288

European-Non Finnish (NFE) AF: 0.519 AC: 35265 AN: 67940

Other (OTH) AF: 0.440 AC: 924 AN: 2102

Alfa AF: 0.502 Hom.: 9548

Bravo AF: 0.430

Asia WGS AF: 0.416 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.66
DANN	Benign	0.56
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs17862241; hg19: chr7-90221348;