chr15-63952544-G-A

Variant names:

• chr15-63952544-G-A
• rs2034099
• NM_014326.5:c.454-13183C>T

Variant summary

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

The NM_014326.5(DAPK2):​c.454-13183C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,134 control chromosomes in the GnomAD database, including 61,868 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 0.90 (61868 hom., cov: 30)
• Consequence: DAPK2 NM_014326.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 1 publications found

Genes affected

DAPK2 (HGNC:2675): (death associated protein kinase 2) This gene encodes a protein that belongs to the serine/threonine protein kinase family. This protein contains a N-terminal protein kinase domain followed by a conserved calmodulin-binding domain with significant similarity to that of death-associated protein kinase 1 (DAPK1), a positive regulator of programmed cell death. Overexpression of this gene was shown to induce cell apoptosis. It uses multiple polyadenylation sites. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014326.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAPK2	NM_014326.5	MANE Select	c.454-13183C>T		intron	N/A	NP_055141.2
	DAPK2	NM_001363730.2		c.454-13183C>T		intron	N/A	NP_001350659.1	Q9UIK4-2
	DAPK2	NM_001384997.1		c.454-13183C>T		intron	N/A	NP_001371926.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAPK2	ENST00000457488.6	TSL:1 MANE Select	c.454-13183C>T		intron	N/A	ENSP00000408277.1	Q9UIK4-1
	DAPK2	ENST00000612884.4	TSL:1	c.454-13183C>T		intron	N/A	ENSP00000484390.1	Q9UIK4-2
	DAPK2	ENST00000558482.5	TSL:1	n.599-13183C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136150 AN: 152016 Hom.: 61833 Cov.: 30

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.895 AC: 136235 AN: 152134 Hom.: 61868 Cov.: 30 AF XY: 0.897 AC XY: 66712 AN XY: 74376

African (AFR) AF: 0.725 AC: 30026 AN: 41420

American (AMR) AF: 0.949 AC: 14519 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3380 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5162 AN: 5174

South Asian (SAS) AF: 0.872 AC: 4212 AN: 4830

European-Finnish (FIN) AF: 0.975 AC: 10334 AN: 10594

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.964 AC: 65577 AN: 68030

Other (OTH) AF: 0.914 AC: 1933 AN: 2114

Alfa AF: 0.942 Hom.: 90455

Bravo AF: 0.888

Asia WGS AF: 0.923 AC: 3208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.084
DANN	Benign	0.67
PhyloP100		-2.4
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: rs2034099; hg19: chr15-64244743;