chr4-970571-C-T

Position:

• chr4-970571-C-T

Variant summary

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

The NM_001347.4(DGKQ):​c.351+422G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0951 in 152,206 control chromosomes in the GnomAD database, including 954 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 0.095 (954 hom., cov: 33)
• Consequence: DGKQ NM_001347.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

Genes affected

DGKQ (HGNC:2856): (diacylglycerol kinase theta) The protein encoded by this gene contains three cysteine-rich domains, a proline-rich region, and a pleckstrin homology domain with an overlapping Ras-associating domain. It is localized in the speckle domains of the nucleus, and mediates the regeneration of phosphatidylinositol (PI) from diacylglycerol in the PI-cycle during cell signal transduction. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DGKQ	NM_001347.4	c.351+422G>A		intron_variant		ENST00000273814.8	NP_001338.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DGKQ	ENST00000273814.8	c.351+422G>A		intron_variant		1	NM_001347.4	ENSP00000273814	P1
DGKQ	ENST00000509465.5	c.191+422G>A		intron_variant		5		ENSP00000425862
DGKQ	ENST00000510286.1	c.126+422G>A		intron_variant		3		ENSP00000427268

Frequencies

GnomAD3 genomes AF: 0.0952 AC: 14474 AN: 152088 Hom.: 955 Cov.: 33

Gnomad AFR AF: 0.0285

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0689

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.0951 AC: 14477 AN: 152206 Hom.: 954 Cov.: 33 AF XY: 0.0990 AC XY: 7367 AN XY: 74398

Gnomad4 AFR AF: 0.0285

Gnomad4 AMR AF: 0.0688

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0978

Alfa AF: 0.110 Hom.: 1732

Bravo AF: 0.0795

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.68
DANN	Benign	0.39

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: rs11248060; hg19: chr4-964359;