rs11038871

Positions:

• chr11-46357892-T-C
• chr11-46357892-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199267.2(DGKZ):​c.162-9399T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,090 control chromosomes in the GnomAD database, including 18,434 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 0.43 (18434 hom., cov: 32)
• Consequence: DGKZ NM_001199267.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

Genes affected

DGKZ (HGNC:2857): (diacylglycerol kinase zeta) The protein encoded by this gene belongs to the eukaryotic diacylglycerol kinase family. It may attenuate protein kinase C activity by regulating diacylglycerol levels in intracellular signaling cascade and signal transduction. Alternative splicing occurs at this locus and multiple transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Nov 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKZ	NM_001199267.2	c.162-9399T>C		intron_variant		ENST00000456247.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKZ	ENST00000456247.7	c.162-9399T>C		intron_variant		1	NM_001199267.2	A1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64771 AN: 151972 Hom.: 18373 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.427 AC: 64885 AN: 152090 Hom.: 18434 Cov.: 32 AF XY: 0.416 AC XY: 30962 AN XY: 74354

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.403

Alfa AF: 0.317 Hom.: 7331

Bravo AF: 0.450

Asia WGS AF: 0.300 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.6
DANN	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs11038871; hg19: chr11-46379442;