9-87643366-T-TTA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_004938.4(DAPK1):c.919-10_919-9insTA variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.038 (440 hom., cov: 0)
  • Exomes 𝑓: 0.0020 (4 hom.)
• Consequence: DAPK1 NM_004938.4 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.631

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 9-87643366-T-TTA is Benign according to our data. Variant chr9-87643366-T-TTA is described in ClinVar as [Benign]. Clinvar id is 776428.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAPK1	NM_004938.4	c.919-10_919-9insTA		splice_polypyrimidine_tract_variant, intron_variant		ENST00000408954.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAPK1	ENST00000408954.8	c.919-10_919-9insTA		splice_polypyrimidine_tract_variant, intron_variant		2	NM_004938.4	P1

Frequencies

GnomAD3 genomes AF: 0.0382 AC: 5262 AN: 137904 Hom.: 439 Cov.: 0

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0147

Gnomad ASJ AF: 0.000295

Gnomad EAS AF: 0.000403

Gnomad SAS AF: 0.000653

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00654

Gnomad NFE AF: 0.00120

Gnomad OTH AF: 0.0212

GnomAD3 exomes AF: 0.00341 AC: 318 AN: 93368 Hom.: 0 AF XY: 0.00301 AC XY: 149 AN XY: 49480

Gnomad AFR exome AF: 0.0375

Gnomad AMR exome AF: 0.00318

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000186

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000184

Gnomad OTH exome AF: 0.00161

GnomAD4 exome AF: 0.00198 AC: 2392 AN: 1209040 Hom.: 4 Cov.: 19 AF XY: 0.00181 AC XY: 1087 AN XY: 600156

Gnomad4 AFR exome AF: 0.0822

Gnomad4 AMR exome AF: 0.00342

Gnomad4 ASJ exome AF: 0.0000487

Gnomad4 EAS exome AF: 0.000359

Gnomad4 SAS exome AF: 0.000285

Gnomad4 FIN exome AF: 0.0000285

Gnomad4 NFE exome AF: 0.000284

Gnomad4 OTH exome AF: 0.00446

GnomAD4 genome AF: 0.0382 AC: 5269 AN: 137940 Hom.: 440 Cov.: 0 AF XY: 0.0360 AC XY: 2420 AN XY: 67308

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0146

Gnomad4 ASJ AF: 0.000295

Gnomad4 EAS AF: 0.000404

Gnomad4 SAS AF: 0.000654

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00120

Gnomad4 OTH AF: 0.0204

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs71354773; hg19: chr9-90258281;