rs1431513

Variant names:

• chr7-14565273-A-G
• rs1431513
• NM_001350709.2:c.1770+8939T>C

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+8939T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,926 control chromosomes in the GnomAD database, including 9,780 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 0.33 (9780 hom., cov: 31)
• Consequence: DGKB NM_001350709.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.666
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKB	NM_001350709.2	c.1770+8939T>C		intron_variant	Intron 20 of 25	ENST00000402815.6	NP_001337638.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKB	ENST00000402815.6	c.1770+8939T>C		intron_variant	Intron 20 of 25	5	NM_001350709.2	ENSP00000384909.1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50514 AN: 151808 Hom.: 9773 Cov.: 31

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.333 AC: 50541 AN: 151926 Hom.: 9780 Cov.: 31 AF XY: 0.336 AC XY: 24923 AN XY: 74244

African (AFR) AF: 0.132 AC: 5486 AN: 41456

American (AMR) AF: 0.416 AC: 6337 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3472

East Asian (EAS) AF: 0.287 AC: 1478 AN: 5148

South Asian (SAS) AF: 0.502 AC: 2417 AN: 4816

European-Finnish (FIN) AF: 0.425 AC: 4484 AN: 10542

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27791 AN: 67940

Other (OTH) AF: 0.331 AC: 698 AN: 2110

Alfa AF: 0.386 Hom.: 8838

Bravo AF: 0.321

Asia WGS AF: 0.397 AC: 1381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.64
PhyloP100		0.67
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: rs1431513; hg19: chr7-14604898;