7-14320384-C-T

Variant summary

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

The NM_001350709.2(DGKB):c.2122+18131G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 152,148 control chromosomes in the GnomAD database, including 633 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 0.086 (633 hom., cov: 32)
• Consequence: DGKB NM_001350709.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

Genes affected

DGKB (HGNC:2850): (diacylglycerol kinase beta) Diacylglycerol kinases (DGKs) are regulators of the intracellular concentration of the second messenger diacylglycerol (DAG) and thus play a key role in cellular processes. Nine mammalian isotypes have been identified, which are encoded by separate genes. Mammalian DGK isozymes contain a conserved catalytic (kinase) domain and a cysteine-rich domain (CRD). The protein encoded by this gene is a diacylglycerol kinase, beta isotype. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKB	NM_001350709.2	c.2122+18131G>A		intron_variant		ENST00000402815.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKB	ENST00000402815.6	c.2122+18131G>A		intron_variant		5	NM_001350709.2	P4

Frequencies

GnomAD3 genomes AF: 0.0865 AC: 13156 AN: 152030 Hom.: 633 Cov.: 32

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0748

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0865 AC: 13156 AN: 152148 Hom.: 633 Cov.: 32 AF XY: 0.0881 AC XY: 6550 AN XY: 74372

Gnomad4 AFR AF: 0.0552

Gnomad4 AMR AF: 0.0747

Gnomad4 ASJ AF: 0.0847

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0993

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0692

Alfa AF: 0.0872 Hom.: 628

Bravo AF: 0.0790

Asia WGS AF: 0.143 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.3
Dann	Benign	0.53

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: rs10215596; hg19: chr7-14360009;