rs2034099

chr15-63952544-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

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 = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAPK2	NM_014326.5	c.454-13183C>T		intron_variant		ENST00000457488.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAPK2	ENST00000457488.6	c.454-13183C>T		intron_variant		1	NM_014326.5	P1

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

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.975

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.914

Alfa AF: 0.951 Hom.: 71392

Bravo AF: 0.888

Asia WGS AF: 0.923 AC: 3208 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	0.084
Dann	Benign	0.67

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: rs2034099; hg19: chr15-64244743;