chr9-87709285-G-A

Variant names:

• chr9-87709285-G-A
• rs3118866
• ENST00000892177.1:c.*1921G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000892177.1(DAPK1):​c.*1921G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,018 control chromosomes in the GnomAD database, including 13,477 homozygotes. 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: 𝑓 0.40 (13477 hom., cov: 32)
• Consequence: DAPK1 ENST00000892177.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 9 publications found

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 Gene-Disease associations (from GenCC):

• autism spectrum disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000892177.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAPK1	ENST00000892177.1		c.*1921G>A		downstream_gene	N/A	ENSP00000562236.1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60916 AN: 151900 Hom.: 13488 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.424

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.401 AC: 60905 AN: 152018 Hom.: 13477 Cov.: 32 AF XY: 0.406 AC XY: 30146 AN XY: 74292

African (AFR) AF: 0.202 AC: 8358 AN: 41478

American (AMR) AF: 0.493 AC: 7524 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1788 AN: 3468

East Asian (EAS) AF: 0.385 AC: 1984 AN: 5152

South Asian (SAS) AF: 0.484 AC: 2334 AN: 4818

European-Finnish (FIN) AF: 0.481 AC: 5087 AN: 10566

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32414 AN: 67954

Other (OTH) AF: 0.423 AC: 889 AN: 2104

Alfa AF: 0.463 Hom.: 28659

Bravo AF: 0.396

Asia WGS AF: 0.452 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs3118866; hg19: chr9-90324200;