rs1880550

Variant names:

• chr7-14734867-A-C
• rs1880550
• NM_001350709.2:c.322+1174T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-14734867-A-C
• chr7-14734867-A-G
• chr7-14734867-A-T

Variant summary

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

The NM_001350709.2(DGKB):​c.322+1174T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,872 control chromosomes in the GnomAD database, including 35,200 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 0.64 (35200 hom., cov: 30)
• Consequence: DGKB NM_001350709.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.808 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.322+1174T>G		intron	N/A	NP_001337638.1	B5MBY2
	DGKB	NM_001350705.1		c.322+1174T>G		intron	N/A	NP_001337634.1	Q9Y6T7-1
	DGKB	NM_001350706.2		c.322+1174T>G		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.322+1174T>G		intron	N/A	ENSP00000384909.1	B5MBY2
	DGKB	ENST00000406247.7	TSL:1	c.322+1174T>G		intron	N/A	ENSP00000386066.3	Q9Y6T7-2
	DGKB	ENST00000399322.7	TSL:5	c.322+1174T>G		intron	N/A	ENSP00000382260.3	Q9Y6T7-1

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97791 AN: 151754 Hom.: 35213 Cov.: 30

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.644 AC: 97784 AN: 151872 Hom.: 35200 Cov.: 30 AF XY: 0.643 AC XY: 47747 AN XY: 74206

African (AFR) AF: 0.310 AC: 12826 AN: 41400

American (AMR) AF: 0.610 AC: 9321 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2879 AN: 3470

East Asian (EAS) AF: 0.565 AC: 2886 AN: 5110

South Asian (SAS) AF: 0.708 AC: 3387 AN: 4784

European-Finnish (FIN) AF: 0.830 AC: 8764 AN: 10560

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55279 AN: 67960

Other (OTH) AF: 0.684 AC: 1446 AN: 2114

Alfa AF: 0.715 Hom.: 15972

Bravo AF: 0.611

Asia WGS AF: 0.619 AC: 2153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.043
DANN	Benign	0.51
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs1880550; hg19: chr7-14774492;