chr19-3958897-C-A

Position:

• chr19-3958897-C-A

Variant summary

Our verdict is Benign. Variant got -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

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=-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/exons	MANE	Protein	UniProt
DAPK3	NM_001348.3	c.*204G>T		3_prime_UTR_variant	9/9	ENST00000545797.7	NP_001339.1
DAPK3	NM_001375658.1	c.*204G>T		3_prime_UTR_variant	9/9		NP_001362587.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAPK3	ENST00000545797.7	c.*204G>T		3_prime_UTR_variant	9/9	2	NM_001348.3	ENSP00000442973	P1
DAPK3	ENST00000301264.7	c.*204G>T		3_prime_UTR_variant	8/8	1		ENSP00000301264	P1
DAPK3	ENST00000595279.1	n.1619G>T		non_coding_transcript_exon_variant	3/3	2

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

Gnomad4 AFR exome AF: 0.311

Gnomad4 AMR exome AF: 0.171

Gnomad4 ASJ exome AF: 0.172

Gnomad4 EAS exome AF: 0.265

Gnomad4 SAS exome AF: 0.191

Gnomad4 FIN exome AF: 0.169

Gnomad4 NFE exome AF: 0.175

Gnomad4 OTH exome AF: 0.190

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

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.207

Alfa AF: 0.195 Hom.: 858

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
DANN	Benign	0.76
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3745982; hg19: chr19-3958895;