rs9525584

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_178009.5(DGKH):​c.855+622T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,072 control chromosomes in the GnomAD database, including 16,500 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 0.45 ( 16500 hom., cov: 32)

Consequence

DGKH
NM_178009.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.565
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DGKHNM_178009.5 linkuse as main transcriptc.855+622T>C intron_variant ENST00000337343.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DGKHENST00000337343.9 linkuse as main transcriptc.855+622T>C intron_variant 1 NM_178009.5 P1Q86XP1-1

Frequencies

GnomAD3 genomes
AF:
0.455
AC:
69088
AN:
151954
Hom.:
16492
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.583
Gnomad AMI
AF:
0.507
Gnomad AMR
AF:
0.307
Gnomad ASJ
AF:
0.344
Gnomad EAS
AF:
0.253
Gnomad SAS
AF:
0.273
Gnomad FIN
AF:
0.451
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.444
Gnomad OTH
AF:
0.433
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.454
AC:
69116
AN:
152072
Hom.:
16500
Cov.:
32
AF XY:
0.447
AC XY:
33255
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.583
Gnomad4 AMR
AF:
0.307
Gnomad4 ASJ
AF:
0.344
Gnomad4 EAS
AF:
0.253
Gnomad4 SAS
AF:
0.272
Gnomad4 FIN
AF:
0.451
Gnomad4 NFE
AF:
0.444
Gnomad4 OTH
AF:
0.432
Alfa
AF:
0.439
Hom.:
7009
Bravo
AF:
0.449
Asia WGS
AF:
0.302
AC:
1051
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.044
DANN
Benign
0.39

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9525584; hg19: chr13-42734894; API