19-3962371-A-G

Position:

• chr19-3962371-A-G

Variant summary

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

The NM_001348.3(DAPK3):​c.630-1210T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,340 control chromosomes in the GnomAD database, including 59,293 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 0.88 (59293 hom., cov: 36)
• Consequence: DAPK3 NM_001348.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793

Genes affected

DAPK3 (HGNC:2676): (death associated protein kinase 3) Death-associated protein kinase 3 (DAPK3) induces morphological changes in apoptosis when overexpressed in mammalian cells. These results suggest that DAPK3 may play a role in the induction of apoptosis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAPK3	NM_001348.3	c.630-1210T>C		intron_variant		ENST00000545797.7
DAPK3	NM_001375658.1	c.630-1210T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAPK3	ENST00000545797.7	c.630-1210T>C		intron_variant		2	NM_001348.3	P1
DAPK3	ENST00000301264.7	c.630-1210T>C		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134196 AN: 152220 Hom.: 59241 Cov.: 36

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.844

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.882 AC: 134309 AN: 152340 Hom.: 59293 Cov.: 36 AF XY: 0.884 AC XY: 65823 AN XY: 74488

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.893

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.868

Gnomad4 OTH AF: 0.873

Alfa AF: 0.865 Hom.: 75746

Bravo AF: 0.885

Asia WGS AF: 0.932 AC: 3238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.27

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: rs10426955; hg19: chr19-3962369;