rs2192879

Variant names:

• chr2-201880915-G-A
• rs2192879
• NM_001366386.2:c.1198+748G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-201880915-G-A
• chr2-201880915-G-C

Variant summary

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

The NM_001366386.2(CDK15):​c.1198+748G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,132 control chromosomes in the GnomAD database, including 53,868 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 0.83 (53868 hom., cov: 31)
• Consequence: CDK15 NM_001366386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 5 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366386.2. 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
	CDK15	NM_001366386.2	MANE Select	c.1198+748G>A		intron	N/A	NP_001353315.1
	CDK15	NM_001261435.1		c.1198+748G>A		intron	N/A	NP_001248364.1
	CDK15	NM_001261436.1		c.1198+748G>A		intron	N/A	NP_001248365.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK15	ENST00000652192.3	MANE Select	c.1198+748G>A		intron	N/A	ENSP00000498608.2
	CDK15	ENST00000450471.6	TSL:1	c.1198+748G>A		intron	N/A	ENSP00000406472.2
	CDK15	ENST00000434439.1	TSL:1	c.1198+748G>A		intron	N/A	ENSP00000412775.1

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126730 AN: 152014 Hom.: 53846 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.834 AC: 126809 AN: 152132 Hom.: 53868 Cov.: 31 AF XY: 0.835 AC XY: 62145 AN XY: 74388

African (AFR) AF: 0.651 AC: 26991 AN: 41458

American (AMR) AF: 0.846 AC: 12935 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3050 AN: 3466

East Asian (EAS) AF: 0.864 AC: 4470 AN: 5172

South Asian (SAS) AF: 0.908 AC: 4368 AN: 4812

European-Finnish (FIN) AF: 0.931 AC: 9862 AN: 10598

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.915 AC: 62258 AN: 68020

Other (OTH) AF: 0.842 AC: 1778 AN: 2112

Alfa AF: 0.889 Hom.: 100219

Bravo AF: 0.818

Asia WGS AF: 0.846 AC: 2940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.3
DANN	Benign	0.66
PhyloP100		-0.10
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: rs2192879; hg19: chr2-202745638;