rs17167930
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001350709.2(DGKB):c.*825A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,520 control chromosomes in the GnomAD database, including 3,220 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 0.19 ( 3214 hom., cov: 33)
Exomes 𝑓: 0.18 ( 6 hom. )
Consequence
DGKB
NM_001350709.2 3_prime_UTR
NM_001350709.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.232
Publications
9 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]
Genome browser will be placed here
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DGKB | NM_001350709.2 | c.*825A>G | 3_prime_UTR_variant | Exon 26 of 26 | ENST00000402815.6 | NP_001337638.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DGKB | ENST00000402815.6 | c.*825A>G | 3_prime_UTR_variant | Exon 26 of 26 | 5 | NM_001350709.2 | ENSP00000384909.1 | |||
DGKB | ENST00000399322.7 | c.*825A>G | 3_prime_UTR_variant | Exon 25 of 25 | 5 | ENSP00000382260.3 | ||||
DGKB | ENST00000403951.6 | c.*825A>G | 3_prime_UTR_variant | Exon 26 of 26 | 5 | ENSP00000385780.2 | ||||
DGKB | ENST00000407950.5 | c.*825A>G | downstream_gene_variant | 5 | ENSP00000385031.1 |
Frequencies
GnomAD3 genomes AF: 0.189 AC: 28692AN: 151968Hom.: 3203 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
28692
AN:
151968
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.177 AC: 77AN: 434Hom.: 6 Cov.: 0 AF XY: 0.192 AC XY: 50AN XY: 260 show subpopulations
GnomAD4 exome
AF:
AC:
77
AN:
434
Hom.:
Cov.:
0
AF XY:
AC XY:
50
AN XY:
260
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
74
AN:
426
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
1
AN:
4
Other (OTH)
AF:
AC:
2
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.478
Heterozygous variant carriers
0
5
10
14
19
24
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.189 AC: 28743AN: 152086Hom.: 3214 Cov.: 33 AF XY: 0.188 AC XY: 13943AN XY: 74358 show subpopulations
GnomAD4 genome
AF:
AC:
28743
AN:
152086
Hom.:
Cov.:
33
AF XY:
AC XY:
13943
AN XY:
74358
show subpopulations
African (AFR)
AF:
AC:
12708
AN:
41462
American (AMR)
AF:
AC:
3008
AN:
15254
Ashkenazi Jewish (ASJ)
AF:
AC:
726
AN:
3470
East Asian (EAS)
AF:
AC:
1109
AN:
5168
South Asian (SAS)
AF:
AC:
480
AN:
4834
European-Finnish (FIN)
AF:
AC:
1462
AN:
10602
Middle Eastern (MID)
AF:
AC:
58
AN:
294
European-Non Finnish (NFE)
AF:
AC:
8591
AN:
67974
Other (OTH)
AF:
AC:
417
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1135
2270
3405
4540
5675
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
288
576
864
1152
1440
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
522
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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