Variant 9-87643366-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004938.4(DAPK1):c.919-10T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00539 in 1,347,374 control chromosomes in the GnomAD database, including 51 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 28 hom., cov: 25)

Exomes 𝑓: 0.0048 ( 23 hom. )

Consequence

DAPK1
NM_004938.4 intron

Scores

Splicing: ADA: 0.8743

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.369

Variant links:

Genes affected

DAPK1 (HGNC:2674): (death associated protein kinase 1) Death-associated protein kinase 1 is a positive mediator of gamma-interferon induced programmed cell death. DAPK1 encodes a structurally unique 160-kD calmodulin dependent serine-threonine kinase that carries 8 ankyrin repeats and 2 putative P-loop consensus sites. It is a tumor suppressor candidate. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

DAPK1 links:

DAPK1 (HGNC:):

DAPK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 9-87643366-T-A is Benign according to our data. Variant chr9-87643366-T-A is described in ClinVar as [Benign]. Clinvar id is 712032.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.074 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAPK1	NM_004938.4 linkuse as main transcript	c.919-10T>A		intron_variant		ENST00000408954.8	NP_004929.2	P53355-1B4DHI4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAPK1	ENST00000408954.8 linkuse as main transcript	c.919-10T>A		intron_variant		2	NM_004938.4	ENSP00000386135.3		P53355-1

Frequencies

GnomAD3 genomes

AF:

0.0107

AC:

1472

AN:

138054

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0367

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00491

Gnomad ASJ

AF:

0.0118

Gnomad EAS

AF:

0.00221

Gnomad SAS

AF:

0.00762

Gnomad FIN

AF:

0.000717

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00186

Gnomad OTH

AF:

0.00581

GnomAD3 exomes

AF:

0.0243

AC:

2270

AN:

93368

Hom.:

AF XY:

0.0204

AC XY:

1010

AN XY:

49480

show subpopulations

Gnomad AFR exome

AF:

0.215

Gnomad AMR exome

AF:

0.0123

Gnomad ASJ exome

AF:

0.0137

Gnomad EAS exome

AF:

0.00711

Gnomad SAS exome

AF:

0.0125

Gnomad FIN exome

AF:

0.00548

Gnomad NFE exome

AF:

0.00669

Gnomad OTH exome

AF:

0.0186

GnomAD4 exome

AF:

0.00479

AC:

5798

AN:

1209284

Hom.:

Cov.:

AF XY:

0.00485

AC XY:

2910

AN XY:

600268

show subpopulations

Gnomad4 AFR exome

AF:

0.0771

Gnomad4 AMR exome

AF:

0.00851

Gnomad4 ASJ exome

AF:

0.00995

Gnomad4 EAS exome

AF:

0.0136

Gnomad4 SAS exome

AF:

0.00755

Gnomad4 FIN exome

AF:

0.00379

Gnomad4 NFE exome

AF:

0.00222

Gnomad4 OTH exome

AF:

0.00826

GnomAD4 genome

AF:

0.0106

AC:

1470

AN:

138090

Hom.:

Cov.:

AF XY:

0.0102

AC XY:

686

AN XY:

67376

show subpopulations

Gnomad4 AFR

AF:

0.0366

Gnomad4 AMR

AF:

0.00490

Gnomad4 ASJ

AF:

0.0118

Gnomad4 EAS

AF:

0.00222

Gnomad4 SAS

AF:

0.00741

Gnomad4 FIN

AF:

0.000717

Gnomad4 NFE

AF:

0.00186

Gnomad4 OTH

AF:

0.00575

Alfa

AF:

0.0147

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.87

dbscSNV1_RF

Benign

0.60

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over