Genetic Variant NM_001350707.2:c.-188+52513A>G (chr7-14922183-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001350707.2(DGKB):c.-188+52513A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 152,076 control chromosomes in the GnomAD database, including 1,592 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 0.081 ( 1592 hom., cov: 32)

Consequence

DGKB
NM_001350707.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.206

Publications

4 publications found

Variant links:

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]

DGKB links:

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new If you want to explore the variant's impact on the transcript NM_001350707.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350707.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
DGKB	NM_001350707.2	c.-188+52513A>G	intron	N/A	NP_001337636.1	B5MBY2
DGKB	NM_001350711.2	c.-188+52513A>G	intron	N/A	NP_001337640.1	B5MCD5
DGKB	NM_001350717.2	c.-188+52513A>G	intron	N/A	NP_001337646.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DGKB	ENST00000910828.1		c.-291-16656A>G	intron	N/A	ENSP00000580887.1
DGKB	ENST00000967726.1		c.-188+52513A>G	intron	N/A	ENSP00000637785.1
DGKB	ENST00000437998.1	TSL:4	c.-188+52513A>G	intron	N/A	ENSP00000405569.1	C9JA18

Frequencies

GnomAD3 genomes

AF:

0.0808

AC:

12285

AN:

151958

Hom.:

1585

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0213

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.0899

Gnomad ASJ

AF:

0.136

Gnomad EAS

AF:

0.637

Gnomad SAS

AF:

0.322

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.0502

Gnomad OTH

AF:

0.0765

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

GnomAD4 genome

AF:

0.0809

AC:

12309

AN:

152076

Hom.:

1592

Cov.:

AF XY:

0.0904

AC XY:

6717

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.0212

AC:

882

AN:

41520

American (AMR)

AF:

0.0903

AC:

1379

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.136

AC:

472

AN:

3466

East Asian (EAS)

AF:

0.638

AC:

3283

AN:

5144

South Asian (SAS)

AF:

0.323

AC:

1553

AN:

4814

European-Finnish (FIN)

AF:

0.103

AC:

1093

AN:

10578

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0502

AC:

3412

AN:

67960

Other (OTH)

AF:

0.0833

AC:

176

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

454

907

1361

1814

2268

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0566

Hom.:

Bravo

AF:

0.0770

Asia WGS

AF:

0.431

AC:

1495

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

7.7

(source)

DANN

Benign

0.47

PhyloP100

0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over