15-63908535-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_014326.5(DAPK2):c.1098G>A(p.Arg366=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,597,812 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00087 ( 1 hom., cov: 32)
Exomes 𝑓: 0.000082 ( 0 hom. )
Consequence
DAPK2
NM_014326.5 synonymous
NM_014326.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.18
Genes affected
DAPK2 (HGNC:2675): (death associated protein kinase 2) This gene encodes a protein that belongs to the serine/threonine protein kinase family. This protein contains a N-terminal protein kinase domain followed by a conserved calmodulin-binding domain with significant similarity to that of death-associated protein kinase 1 (DAPK1), a positive regulator of programmed cell death. Overexpression of this gene was shown to induce cell apoptosis. It uses multiple polyadenylation sites. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
?
Variant 15-63908535-C-T is Benign according to our data. Variant chr15-63908535-C-T is described in ClinVar as [Benign]. Clinvar id is 741212.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.18 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAPK2 | NM_014326.5 | c.1098G>A | p.Arg366= | synonymous_variant | 12/12 | ENST00000457488.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAPK2 | ENST00000457488.6 | c.1098G>A | p.Arg366= | synonymous_variant | 12/12 | 1 | NM_014326.5 | P1 | |
DAPK2 | ENST00000261891.7 | c.1098G>A | p.Arg366= | synonymous_variant | 11/11 | 2 | P1 | ||
DAPK2 | ENST00000559731.5 | n.257G>A | non_coding_transcript_exon_variant | 4/4 | 5 | ||||
DAPK2 | ENST00000559007.5 | c.*3054G>A | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000815 AC: 124AN: 152190Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
124
AN:
152190
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000183 AC: 41AN: 223804Hom.: 0 AF XY: 0.000133 AC XY: 16AN XY: 120192
GnomAD3 exomes
AF:
AC:
41
AN:
223804
Hom.:
AF XY:
AC XY:
16
AN XY:
120192
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000816 AC: 118AN: 1445504Hom.: 0 Cov.: 30 AF XY: 0.0000669 AC XY: 48AN XY: 717386
GnomAD4 exome
AF:
AC:
118
AN:
1445504
Hom.:
Cov.:
30
AF XY:
AC XY:
48
AN XY:
717386
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000867 AC: 132AN: 152308Hom.: 1 Cov.: 32 AF XY: 0.000873 AC XY: 65AN XY: 74480
GnomAD4 genome
?
AF:
AC:
132
AN:
152308
Hom.:
Cov.:
32
AF XY:
AC XY:
65
AN XY:
74480
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 20, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at