rs10241087

chr7-14234718-A-Gchr7-14234718-A-T

Variant summary

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

The NM_001350709.2(DGKB):c.2123-56567T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,952 control chromosomes in the GnomAD database, including 7,014 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 0.26 (7014 hom., cov: 32)
• Consequence: DGKB NM_001350709.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKB	NM_001350709.2	c.2123-56567T>C		intron_variant		ENST00000402815.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKB	ENST00000402815.6	c.2123-56567T>C		intron_variant		5	NM_001350709.2	P4

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39417 AN: 151832 Hom.: 7004 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0912

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.260 AC: 39472 AN: 151952 Hom.: 7014 Cov.: 32 AF XY: 0.260 AC XY: 19291 AN XY: 74276

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0918

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.211

Alfa AF: 0.168 Hom.: 3474

Bravo AF: 0.265

Asia WGS AF: 0.152 AC: 529 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	15
Dann	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10241087; hg19: chr7-14274343;