chr4-970571-C-T

Variant names:

• chr4-970571-C-T
• rs11248060
• NM_001347.4:c.351+422G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 64 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001347.4. 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
	DGKQ	NM_001347.4	MANE Select	c.351+422G>A		intron	N/A	NP_001338.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKQ	ENST00000273814.8	TSL:1 MANE Select	c.351+422G>A		intron	N/A	ENSP00000273814.3
	DGKQ	ENST00000509465.5	TSL:5	c.189+422G>A		intron	N/A	ENSP00000425862.1
	DGKQ	ENST00000510286.1	TSL:3	c.126+422G>A		intron	N/A	ENSP00000427268.1

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

African (AFR) AF: 0.0285 AC: 1185 AN: 41560

American (AMR) AF: 0.0688 AC: 1051 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3468

East Asian (EAS) AF: 0.117 AC: 605 AN: 5170

South Asian (SAS) AF: 0.218 AC: 1050 AN: 4816

European-Finnish (FIN) AF: 0.170 AC: 1796 AN: 10590

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7712 AN: 68000

Other (OTH) AF: 0.0978 AC: 207 AN: 2116

Alfa AF: 0.106 Hom.: 3650

Bravo AF: 0.0795

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.68
DANN	Benign	0.39
PhyloP100		-0.29
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: rs11248060; hg19: chr4-964359;