rs11038871

Variant names:

• chr11-46357892-T-C
• rs11038871
• NM_001199267.2:c.162-9399T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199267.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKZ	NM_001199267.2	MANE Select	c.162-9399T>C		intron	N/A	NP_001186196.1
	DGKZ	NM_201532.3		c.213-9399T>C		intron	N/A	NP_963290.1
	DGKZ	NM_001199266.2		c.162-9399T>C		intron	N/A	NP_001186195.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKZ	ENST00000456247.7	TSL:1 MANE Select	c.162-9399T>C		intron	N/A	ENSP00000395684.2
	DGKZ	ENST00000527911.5	TSL:1	c.162-9399T>C		intron	N/A	ENSP00000436291.1
	DGKZ	ENST00000421244.6	TSL:1	c.162-9399T>C		intron	N/A	ENSP00000391021.2

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

African (AFR) AF: 0.812 AC: 33690 AN: 41486

American (AMR) AF: 0.285 AC: 4346 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3470

East Asian (EAS) AF: 0.180 AC: 932 AN: 5184

South Asian (SAS) AF: 0.332 AC: 1600 AN: 4816

European-Finnish (FIN) AF: 0.165 AC: 1749 AN: 10598

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19977 AN: 67954

Other (OTH) AF: 0.403 AC: 850 AN: 2110

Alfa AF: 0.360 Hom.: 20007

Bravo AF: 0.450

Asia WGS AF: 0.300 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.6
DANN	Benign	0.64
PhyloP100		-0.14
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: rs11038871; hg19: chr11-46379442;