NM_001350709.2:c.*825A>G

Variant names:

• chr7-14148306-T-C
• rs17167930
• NM_001350709.2:c.*825A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001350709.2(DGKB):​c.*825A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,520 control chromosomes in the GnomAD database, including 3,220 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 0.19 (3214 hom., cov: 33)
  • Exomes 𝑓: 0.18 (6 hom.)
• Consequence: DGKB NM_001350709.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350709.2. 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
	DGKB	NM_001350709.2	MANE Select	c.*825A>G		3_prime_UTR	Exon 26 of 26	NP_001337638.1
	DGKB	NM_001350705.1		c.*825A>G		3_prime_UTR	Exon 26 of 26	NP_001337634.1
	DGKB	NM_001350706.2		c.*825A>G		3_prime_UTR	Exon 26 of 26	NP_001337635.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKB	ENST00000402815.6	TSL:5 MANE Select	c.*825A>G		3_prime_UTR	Exon 26 of 26	ENSP00000384909.1
	DGKB	ENST00000399322.7	TSL:5	c.*825A>G		3_prime_UTR	Exon 25 of 25	ENSP00000382260.3
	DGKB	ENST00000403951.6	TSL:5	c.*825A>G		3_prime_UTR	Exon 26 of 26	ENSP00000385780.2

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28692 AN: 151968 Hom.: 3203 Cov.: 33

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.0996

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.199

GnomAD4 exome AF: 0.177 AC: 77 AN: 434 Hom.: 6 Cov.: 0 AF XY: 0.192 AC XY: 50 AN XY: 260

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.174 AC: 74 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.189 AC: 28743 AN: 152086 Hom.: 3214 Cov.: 33 AF XY: 0.188 AC XY: 13943 AN XY: 74358

African (AFR) AF: 0.306 AC: 12708 AN: 41462

American (AMR) AF: 0.197 AC: 3008 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1109 AN: 5168

South Asian (SAS) AF: 0.0993 AC: 480 AN: 4834

European-Finnish (FIN) AF: 0.138 AC: 1462 AN: 10602

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8591 AN: 67974

Other (OTH) AF: 0.197 AC: 417 AN: 2116

Alfa AF: 0.149 Hom.: 3765

Bravo AF: 0.202

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.79
PhyloP100		0.23
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: rs17167930; hg19: chr7-14187931;