7-14554611-C-T

Variant names:

• chr7-14554611-C-T
• rs1367782
• NM_001350709.2:c.1770+19601G>A

Variant summary

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

The NM_001350709.2(DGKB):​c.1770+19601G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,788 control chromosomes in the GnomAD database, including 24,629 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 0.57 (24629 hom., cov: 31)
• Consequence: DGKB NM_001350709.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKB	NM_001350709.2	MANE Select	c.1770+19601G>A		intron	N/A	NP_001337638.1	B5MBY2
	DGKB	NM_001350705.1		c.1773+19601G>A		intron	N/A	NP_001337634.1	Q9Y6T7-1
	DGKB	NM_001350706.2		c.1773+19601G>A		intron	N/A	NP_001337635.1	Q9Y6T7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKB	ENST00000402815.6	TSL:5 MANE Select	c.1770+19601G>A		intron	N/A	ENSP00000384909.1	B5MBY2
	DGKB	ENST00000406247.7	TSL:1	c.1773+19601G>A		intron	N/A	ENSP00000386066.3	Q9Y6T7-2
	DGKB	ENST00000399322.7	TSL:5	c.1773+19601G>A		intron	N/A	ENSP00000382260.3	Q9Y6T7-1

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85728 AN: 151672 Hom.: 24576 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.565 AC: 85835 AN: 151788 Hom.: 24629 Cov.: 31 AF XY: 0.574 AC XY: 42576 AN XY: 74154

African (AFR) AF: 0.583 AC: 24145 AN: 41394

American (AMR) AF: 0.610 AC: 9313 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1761 AN: 3466

East Asian (EAS) AF: 0.844 AC: 4356 AN: 5160

South Asian (SAS) AF: 0.578 AC: 2779 AN: 4808

European-Finnish (FIN) AF: 0.638 AC: 6708 AN: 10512

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35001 AN: 67872

Other (OTH) AF: 0.538 AC: 1138 AN: 2114

Alfa AF: 0.540 Hom.: 2790

Bravo AF: 0.569

Asia WGS AF: 0.699 AC: 2403 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.044
DANN	Benign	0.14
PhyloP100		-1.6
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: rs1367782; hg19: chr7-14594236;