Genetic Variant DGKB:c.1771-24986A>C (chr7-14503211-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001350709.2(DGKB):c.1771-24986A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,058 control chromosomes in the GnomAD database, including 4,390 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 0.20 ( 4390 hom., cov: 32)

Consequence

DGKB
NM_001350709.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.251

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_001350709.2, 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DGKB	NM_001350709.2	MANE Select	c.1771-24986A>C	intron	N/A	NP_001337638.1	B5MBY2
DGKB	NM_001350705.1		c.1774-24986A>C	intron	N/A	NP_001337634.1	Q9Y6T7-1
DGKB	NM_001350706.2		c.1774-24986A>C	intron	N/A	NP_001337635.1	Q9Y6T7-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DGKB	ENST00000402815.6	TSL:5 MANE Select	c.1771-24986A>C	intron	N/A	ENSP00000384909.1	B5MBY2
DGKB	ENST00000406247.7	TSL:1	c.1774-24986A>C	intron	N/A	ENSP00000386066.3	Q9Y6T7-2
DGKB	ENST00000399322.7	TSL:5	c.1774-24986A>C	intron	N/A	ENSP00000382260.3	Q9Y6T7-1

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30548

AN:

151942

Hom.:

4375

Cov.:

show subpopulations

Gnomad AFR

AF:

0.365

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.143

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.550

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0985

Gnomad OTH

AF:

0.185

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

GnomAD4 genome

AF:

0.201

AC:

30602

AN:

152058

Hom.:

4390

Cov.:

AF XY:

0.207

AC XY:

15408

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.366

AC:

15169

AN:

41454

American (AMR)

AF:

0.143

AC:

2176

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

424

AN:

3470

East Asian (EAS)

AF:

0.549

AC:

2833

AN:

5162

South Asian (SAS)

AF:

0.154

AC:

745

AN:

4828

European-Finnish (FIN)

AF:

0.189

AC:

2001

AN:

10598

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0985

AC:

6697

AN:

67968

Other (OTH)

AF:

0.184

AC:

388

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1128

2257

3385

4514

5642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.108

Hom.:

638

Bravo

AF:

0.210

Asia WGS

AF:

0.308

AC:

1072

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.4

(source)

DANN

Benign

0.78

PhyloP100

0.25

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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