Variant chr9-87643367-A-T 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.919-9A>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.054 ( 41 hom., cov: 0)

Exomes 𝑓: 0.011 ( 39 hom. )

Consequence

DAPK1
NM_004938.4 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.001058

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.631

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:

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=-0.69).

BP6

Variant 9-87643367-A-T is Benign according to our data. Variant chr9-87643367-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 712484.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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.919-9A>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000408954.8	NP_004929.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAPK1	ENST00000408954.8 linkuse as main transcript	c.919-9A>T		splice_polypyrimidine_tract_variant, intron_variant		2	NM_004938.4	ENSP00000386135	P1	P53355-1

Frequencies

GnomAD3 genomes

AF:

0.0540

AC:

2458

AN:

45482

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.225

Gnomad AMI

AF:

0.0315

Gnomad AMR

AF:

0.0205

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.0585

Gnomad SAS

AF:

0.00547

Gnomad FIN

AF:

0.0112

Gnomad MID

AF:

0.0556

Gnomad NFE

AF:

0.0226

Gnomad OTH

AF:

0.0317

GnomAD3 exomes

AF:

0.0168

AC:

1393

AN:

82894

Hom.:

AF XY:

0.0147

AC XY:

675

AN XY:

46002

show subpopulations

Gnomad AFR exome

AF:

0.118

Gnomad AMR exome

AF:

0.00927

Gnomad ASJ exome

AF:

0.00429

Gnomad EAS exome

AF:

0.0411

Gnomad SAS exome

AF:

0.00520

Gnomad FIN exome

AF:

0.0131

Gnomad NFE exome

AF:

0.0106

Gnomad OTH exome

AF:

0.0158

GnomAD4 exome

AF:

0.0113

AC:

9086

AN:

804590

Hom.:

Cov.:

AF XY:

0.0110

AC XY:

4353

AN XY:

396922

show subpopulations

Gnomad4 AFR exome

AF:

0.0703

Gnomad4 AMR exome

AF:

0.00895

Gnomad4 ASJ exome

AF:

0.00497

Gnomad4 EAS exome

AF:

0.0348

Gnomad4 SAS exome

AF:

0.00582

Gnomad4 FIN exome

AF:

0.0122

Gnomad4 NFE exome

AF:

0.00925

Gnomad4 OTH exome

AF:

0.0120

GnomAD4 genome

AF:

0.0541

AC:

2460

AN:

45504

Hom.:

Cov.:

AF XY:

0.0515

AC XY:

1155

AN XY:

22406

show subpopulations

Gnomad4 AFR

AF:

0.225

Gnomad4 AMR

AF:

0.0205

Gnomad4 ASJ

AF:

0.0150

Gnomad4 EAS

AF:

0.0582

Gnomad4 SAS

AF:

0.00550

Gnomad4 FIN

AF:

0.0112

Gnomad4 NFE

AF:

0.0226

Gnomad4 OTH

AF:

0.0313

Alfa

AF:

0.0422

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Likely 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

-0.69

CADD

Benign

7.3

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0011

dbscSNV1_RF

Benign

0.078

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