15-64020956-G-C

Position:

• chr15-64020956-G-C

Variant summary

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

The NM_014326.5(DAPK2):​c.92+19214C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,196 control chromosomes in the GnomAD database, including 51,984 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 0.82 (51984 hom., cov: 32)
• Consequence: DAPK2 NM_014326.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

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]

DAPK2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAPK2	NM_014326.5	c.92+19214C>G		intron_variant		ENST00000457488.6	NP_055141.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAPK2	ENST00000457488.6	c.92+19214C>G		intron_variant		1	NM_014326.5	ENSP00000408277.1

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125330 AN: 152078 Hom.: 51955 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.824 AC: 125407 AN: 152196 Hom.: 51984 Cov.: 32 AF XY: 0.822 AC XY: 61186 AN XY: 74408

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.841

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.814

Alfa AF: 0.824 Hom.: 3008

Bravo AF: 0.826

Asia WGS AF: 0.799 AC: 2778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.95
DANN	Benign	0.54

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: rs184556; hg19: chr15-64313155;