19-3962371-A-G

Variant names:

• chr19-3962371-A-G
• rs10426955
• NM_001348.3:c.630-1210T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001348.3. 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
	DAPK3	NM_001348.3	MANE Select	c.630-1210T>C		intron	N/A	NP_001339.1	O43293-1
	DAPK3	NM_001375658.1		c.630-1210T>C		intron	N/A	NP_001362587.1	O43293-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAPK3	ENST00000545797.7	TSL:2 MANE Select	c.630-1210T>C		intron	N/A	ENSP00000442973.1	O43293-1
	DAPK3	ENST00000301264.7	TSL:1	c.630-1210T>C		intron	N/A	ENSP00000301264.3	O43293-1
	DAPK3	ENST00000875568.1		c.630-1210T>C		intron	N/A	ENSP00000545627.1

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

African (AFR) AF: 0.892 AC: 37095 AN: 41578

American (AMR) AF: 0.909 AC: 13911 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2783 AN: 3472

East Asian (EAS) AF: 0.993 AC: 5151 AN: 5188

South Asian (SAS) AF: 0.893 AC: 4315 AN: 4832

European-Finnish (FIN) AF: 0.856 AC: 9077 AN: 10606

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.868 AC: 59096 AN: 68046

Other (OTH) AF: 0.873 AC: 1847 AN: 2116

Alfa AF: 0.867 Hom.: 102218

Bravo AF: 0.885

Asia WGS AF: 0.932 AC: 3238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.27
PhyloP100		-0.79
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: rs10426955; hg19: chr19-3962369;