rs749468

chr15-63918080-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000612884.4(DAPK2):c.*4655G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,916 control chromosomes in the GnomAD database, including 20,509 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 0.51 (20506 hom., cov: 31)
  • Exomes 𝑓: 0.55 (3 hom.)
• Consequence: DAPK2 ENST00000612884.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAPK2	NM_014326.5	c.859-5883G>A		intron_variant		ENST00000457488.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAPK2	ENST00000457488.6	c.859-5883G>A		intron_variant		1	NM_014326.5	P1

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77266 AN: 151776 Hom.: 20495 Cov.: 31

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.514

GnomAD4 exome AF: 0.545 AC: 12 AN: 22 Hom.: 3 Cov.: 0 AF XY: 0.600 AC XY: 6 AN XY: 10

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.643

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.509 AC: 77301 AN: 151894 Hom.: 20506 Cov.: 31 AF XY: 0.514 AC XY: 38133 AN XY: 74208

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.520

Alfa AF: 0.515 Hom.: 4599

Bravo AF: 0.507

Asia WGS AF: 0.781 AC: 2713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	13
Dann	Benign	0.79

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: rs749468; hg19: chr15-64210279;