2-201822291-T-C

Position:

• chr2-201822291-T-C

Variant summary

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

The NM_001366386.2(CDK15):​c.449-518T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 152,240 control chromosomes in the GnomAD database, including 63,421 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 (63421 hom., cov: 32)
• Consequence: CDK15 NM_001366386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

Genes affected

CDK15 (HGNC:14434): (cyclin dependent kinase 15) Enables protein serine/threonine kinase activity. Predicted to be involved in protein phosphorylation and regulation of transcription involved in G1/S transition of mitotic cell cycle. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

CDK15 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDK15	NM_001366386.2	c.449-518T>C		intron_variant		ENST00000652192.3	NP_001353315.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDK15	ENST00000652192.3	c.449-518T>C		intron_variant			NM_001366386.2	ENSP00000498608.2

Frequencies

GnomAD3 genomes AF: 0.909 AC: 138250 AN: 152122 Hom.: 63390 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.920

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.909 AC: 138334 AN: 152240 Hom.: 63421 Cov.: 32 AF XY: 0.910 AC XY: 67750 AN XY: 74432

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.957

Gnomad4 ASJ AF: 0.972

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.954

Gnomad4 NFE AF: 0.960

Gnomad4 OTH AF: 0.921

Alfa AF: 0.954 Hom.: 87241

Bravo AF: 0.904

Asia WGS AF: 0.969 AC: 3368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.50

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: rs7585095; hg19: chr2-202687014;