Genetic Variant DAPK3:c.*204G>A (chr19-3958897-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001348.3(DAPK3):c.*204G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000232 in 430,772 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.0000023 ( 0 hom. )

Consequence

DAPK3
NM_001348.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.85

Publications

0 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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAPK3	NM_001348.3 link	c.*204G>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000545797.7	NP_001339.1	O43293-1B3KNJ3
DAPK3	NM_001375658.1 link	c.*204G>A		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>A	3_prime_UTR_variant	Exon 9 of 9	2	NM_001348.3	ENSP00000442973.1	O43293-1
DAPK3	ENST00000301264.7 link	c.*204G>A	3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000301264.3	O43293-1
DAPK3	ENST00000595279.1 link	n.1619G>A	non_coding_transcript_exon_variant	Exon 3 of 3	2
ENSG00000294388	ENST00000723280.1 link	n.1768-1741C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000232

AC:

AN:

430772

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

226366

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10788

American (AMR)

AF:

0.00

AC:

AN:

16834

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

13112

East Asian (EAS)

AF:

0.00

AC:

AN:

29222

South Asian (SAS)

AF:

0.00

AC:

AN:

43226

European-Finnish (FIN)

AF:

0.00

AC:

AN:

29354

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1904

European-Non Finnish (NFE)

AF:

0.00000383

AC:

AN:

261188

Other (OTH)

AF:

0.00

AC:

AN:

25144

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.5

(source)

DANN

Benign

0.74

PhyloP100

1.9

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over