Genetic Variant DAPK3:c.*204G>T (chr19-3958897-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001348.3(DAPK3):c.*204G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 582,590 control chromosomes in the GnomAD database, including 11,930 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 0.22 ( 3948 hom., cov: 32)

Exomes 𝑓: 0.19 ( 7982 hom. )

Consequence

DAPK3
NM_001348.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.85

Publications

12 publications found

Variant links:

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]

DAPK3 links:

ENSG00000294388 (HGNC:):

ENSG00000294388 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAPK3	NM_001348.3 link	c.*204G>T		3_prime_UTR_variant	Exon 9 of 9	ENST00000545797.7	NP_001339.1	O43293-1B3KNJ3
DAPK3	NM_001375658.1 link	c.*204G>T		3_prime_UTR_variant	Exon 9 of 9		NP_001362587.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DAPK3	ENST00000545797.7 link	c.*204G>T	3_prime_UTR_variant	Exon 9 of 9	2	NM_001348.3	ENSP00000442973.1	O43293-1
DAPK3	ENST00000301264.7 link	c.*204G>T	3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000301264.3	O43293-1
DAPK3	ENST00000595279.1 link	n.1619G>T	non_coding_transcript_exon_variant	Exon 3 of 3	2
ENSG00000294388	ENST00000723280.1 link	n.1768-1741C>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

32918

AN:

151988

Hom.:

3938

Cov.:

show subpopulations

Gnomad AFR

AF:

0.317

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.176

Gnomad EAS

AF:

0.195

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.180

Gnomad OTH

AF:

0.208

GnomAD4 exome

AF:

0.186

AC:

80250

AN:

430484

Hom.:

7982

Cov.:

AF XY:

0.187

AC XY:

42269

AN XY:

226248

show subpopulations

African (AFR)

AF:

0.311

AC:

3353

AN:

10778

American (AMR)

AF:

0.171

AC:

2881

AN:

16820

Ashkenazi Jewish (ASJ)

AF:

0.172

AC:

2255

AN:

13106

East Asian (EAS)

AF:

0.265

AC:

7738

AN:

29196

South Asian (SAS)

AF:

0.191

AC:

8265

AN:

43174

European-Finnish (FIN)

AF:

0.169

AC:

4946

AN:

29342

Middle Eastern (MID)

AF:

0.224

AC:

426

AN:

1904

European-Non Finnish (NFE)

AF:

0.175

AC:

45598

AN:

261030

Other (OTH)

AF:

0.190

AC:

4788

AN:

25134

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

3160

6320

9479

12639

15799

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

298

596

894

1192

1490

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.217

AC:

32946

AN:

152106

Hom.:

3948

Cov.:

AF XY:

0.215

AC XY:

15981

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.317

AC:

13140

AN:

41476

American (AMR)

AF:

0.169

AC:

2589

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.176

AC:

612

AN:

3468

East Asian (EAS)

AF:

0.195

AC:

1007

AN:

5154

South Asian (SAS)

AF:

0.178

AC:

860

AN:

4826

European-Finnish (FIN)

AF:

0.173

AC:

1829

AN:

10602

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.180

AC:

12218

AN:

67968

Other (OTH)

AF:

0.207

AC:

436

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

1258

2516

3773

5031

6289

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.200

Hom.:

1002

Bravo

AF:

0.220

Asia WGS

AF:

0.211

AC:

733

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.0

(source)

DANN

Benign

0.76

PhyloP100

1.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over