7-14382290-A-T

Variant names:

• chr7-14382290-A-T
• rs12699612
• NM_001350709.2:c.1836-36899T>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.1836-36899T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 148,532 control chromosomes in the GnomAD database, including 33,452 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 0.67 (33452 hom., cov: 30)
• Consequence: DGKB NM_001350709.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• 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]

LOC105375164 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKB	NM_001350709.2	c.1836-36899T>A		intron_variant	Intron 21 of 25	ENST00000402815.6	NP_001337638.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKB	ENST00000402815.6	c.1836-36899T>A		intron_variant	Intron 21 of 25	5	NM_001350709.2	ENSP00000384909.1

Frequencies

GnomAD3 genomes AF: 0.665 AC: 98768 AN: 148444 Hom.: 33451 Cov.: 30

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.824

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.665 AC: 98805 AN: 148532 Hom.: 33452 Cov.: 30 AF XY: 0.664 AC XY: 48114 AN XY: 72442

African (AFR) AF: 0.491 AC: 19276 AN: 39234

American (AMR) AF: 0.645 AC: 9705 AN: 15056

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2352 AN: 3460

East Asian (EAS) AF: 0.716 AC: 3649 AN: 5094

South Asian (SAS) AF: 0.679 AC: 3242 AN: 4772

European-Finnish (FIN) AF: 0.749 AC: 7597 AN: 10148

Middle Eastern (MID) AF: 0.606 AC: 171 AN: 282

European-Non Finnish (NFE) AF: 0.751 AC: 50677 AN: 67508

Other (OTH) AF: 0.670 AC: 1386 AN: 2068

Alfa AF: 0.631 Hom.: 2228

Bravo AF: 0.644

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.31
PhyloP100		-1.4
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: rs12699612; hg19: chr7-14421915;