rs17167930
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Variant summary
Our verdict is Benign. Variant got -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
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGKB | NM_001350709.2 | c.*825A>G | 3_prime_UTR_variant | 26/26 | ENST00000402815.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGKB | ENST00000402815.6 | c.*825A>G | 3_prime_UTR_variant | 26/26 | 5 | NM_001350709.2 | P4 | ||
DGKB | ENST00000399322.7 | c.*825A>G | 3_prime_UTR_variant | 25/25 | 5 | A1 | |||
DGKB | ENST00000403951.6 | c.*825A>G | 3_prime_UTR_variant | 26/26 | 5 | A1 | |||
DGKB | ENST00000407950.5 | downstream_gene_variant | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.189 AC: 28692AN: 151968Hom.: 3203 Cov.: 33
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GnomAD4 exome AF: 0.177 AC: 77AN: 434Hom.: 6 Cov.: 0 AF XY: 0.192 AC XY: 50AN XY: 260
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GnomAD4 genome ? AF: 0.189 AC: 28743AN: 152086Hom.: 3214 Cov.: 33 AF XY: 0.188 AC XY: 13943AN XY: 74358
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at