rs1886811

Variant names:

• chr13-42147928-A-G
• rs1886811
• NM_178009.5:c.385-7363A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178009.5(DGKH):​c.385-7363A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,064 control chromosomes in the GnomAD database, including 10,979 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 0.36 (10979 hom., cov: 32)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKH	NM_178009.5	c.385-7363A>G		intron_variant	Intron 3 of 29	ENST00000337343.9	NP_821077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKH	ENST00000337343.9	c.385-7363A>G		intron_variant	Intron 3 of 29	1	NM_178009.5	ENSP00000337572.4

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55233 AN: 151946 Hom.: 10963 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.364 AC: 55293 AN: 152064 Hom.: 10979 Cov.: 32 AF XY: 0.365 AC XY: 27155 AN XY: 74324

African (AFR) AF: 0.212 AC: 8785 AN: 41494

American (AMR) AF: 0.441 AC: 6731 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1447 AN: 3466

East Asian (EAS) AF: 0.187 AC: 971 AN: 5188

South Asian (SAS) AF: 0.453 AC: 2179 AN: 4810

European-Finnish (FIN) AF: 0.400 AC: 4211 AN: 10538

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29733 AN: 67980

Other (OTH) AF: 0.389 AC: 821 AN: 2108

Alfa AF: 0.393 Hom.: 2032

Bravo AF: 0.360

Asia WGS AF: 0.308 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.46
PhyloP100		-0.014
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1886811; hg19: chr13-42722064;