rs1170188
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_178009.5(DGKH):c.193-22628A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,132 control chromosomes in the GnomAD database, including 50,665 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 0.81 ( 50665 hom., cov: 31)
Consequence
DGKH
NM_178009.5 intron
NM_178009.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.161
Genes affected
DGKH (HGNC:2854): (diacylglycerol kinase eta) This gene encodes a member of the diacylglycerol kinase (DGK) enzyme family. Members of this family are involved in regulating intracellular concentrations of diacylglycerol and phosphatidic acid. Variation in this gene has been associated with bipolar disorder. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Jul 2014]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGKH | NM_178009.5 | c.193-22628A>G | intron_variant | ENST00000337343.9 | |||
DGKH | NM_001204504.3 | c.193-22628A>G | intron_variant | ||||
DGKH | NM_152910.6 | c.193-22628A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGKH | ENST00000337343.9 | c.193-22628A>G | intron_variant | 1 | NM_178009.5 | P1 | |||
DGKH | ENST00000261491.9 | c.193-22628A>G | intron_variant | 1 | |||||
DGKH | ENST00000379274.6 | c.193-22628A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.811 AC: 123337AN: 152014Hom.: 50612 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.811 AC: 123450AN: 152132Hom.: 50665 Cov.: 31 AF XY: 0.805 AC XY: 59811AN XY: 74328
GnomAD4 genome
?
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123450
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31
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59811
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74328
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2378
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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