NM_001348.3:c.*204G>T

Variant names:

• chr19-3958897-C-A
• rs3745982
• NM_001348.3:c.*204G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85
• Publications: 12 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]

ENSG00000294388 (HGNC:):

ACMG classification

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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAPK3	NM_001348.3	MANE Select	c.*204G>T		3_prime_UTR	Exon 9 of 9	NP_001339.1
	DAPK3	NM_001375658.1		c.*204G>T		3_prime_UTR	Exon 9 of 9	NP_001362587.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAPK3	ENST00000545797.7	TSL:2 MANE Select	c.*204G>T		3_prime_UTR	Exon 9 of 9	ENSP00000442973.1
	DAPK3	ENST00000301264.7	TSL:1	c.*204G>T		3_prime_UTR	Exon 8 of 8	ENSP00000301264.3
	DAPK3	ENST00000595279.1	TSL:2	n.1619G>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32918 AN: 151988 Hom.: 3938 Cov.: 32

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.: 3 AF XY: 0.187 AC XY: 42269 AN XY: 226248

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

GnomAD4 genome AF: 0.217 AC: 32946 AN: 152106 Hom.: 3948 Cov.: 32 AF XY: 0.215 AC XY: 15981 AN XY: 74354

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: 81 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12218 AN: 67968

Other (OTH) AF: 0.207 AC: 436 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
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)

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: rs3745982; hg19: chr19-3958895;