rs3095748

Variant names:

• chr9-87594222-G-A
• rs3095748
• NM_004938.4:c.63-10732G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-87594222-G-A
• chr9-87594222-G-C
• chr9-87594222-G-T

Variant summary

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

The NM_004938.4(DAPK1):​c.63-10732G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.931 in 152,208 control chromosomes in the GnomAD database, including 66,105 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 0.93 (66105 hom., cov: 31)
• Consequence: DAPK1 NM_004938.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 10 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAPK1	NM_004938.4	c.63-10732G>A		intron_variant	Intron 2 of 25	ENST00000408954.8	NP_004929.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAPK1	ENST00000408954.8	c.63-10732G>A		intron_variant	Intron 2 of 25	2	NM_004938.4	ENSP00000386135.3

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141611 AN: 152090 Hom.: 66042 Cov.: 31

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.931 AC: 141734 AN: 152208 Hom.: 66105 Cov.: 31 AF XY: 0.930 AC XY: 69156 AN XY: 74400

African (AFR) AF: 0.966 AC: 40126 AN: 41550

American (AMR) AF: 0.922 AC: 14105 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3166 AN: 3468

East Asian (EAS) AF: 0.777 AC: 4009 AN: 5162

South Asian (SAS) AF: 0.891 AC: 4302 AN: 4826

European-Finnish (FIN) AF: 0.922 AC: 9747 AN: 10576

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63218 AN: 68010

Other (OTH) AF: 0.926 AC: 1955 AN: 2112

Alfa AF: 0.926 Hom.: 275025

Bravo AF: 0.933

Asia WGS AF: 0.873 AC: 3036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.029
DANN	Benign	0.66
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
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

Other links and lift over

dbSNP: rs3095748; hg19: chr9-90209137;