13-42123671-G-C

Variant names:

• chr13-42123671-G-C
• rs1170169
• NM_178009.5:c.193-3792G>C

Variant summary

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

The NM_178009.5(DGKH):​c.193-3792G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,070 control chromosomes in the GnomAD database, including 35,208 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 0.67 (35208 hom., cov: 33)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178009.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKH	NM_178009.5	MANE Select	c.193-3792G>C		intron	N/A	NP_821077.1	Q86XP1-1
	DGKH	NM_001204504.3		c.193-3792G>C		intron	N/A	NP_001191433.1	Q86XP1-2
	DGKH	NM_152910.6		c.193-3792G>C		intron	N/A	NP_690874.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKH	ENST00000337343.9	TSL:1 MANE Select	c.193-3792G>C		intron	N/A	ENSP00000337572.4	Q86XP1-1
	DGKH	ENST00000261491.9	TSL:1	c.193-3792G>C		intron	N/A	ENSP00000261491.4	Q86XP1-2
	DGKH	ENST00000916518.1		c.193-3792G>C		intron	N/A	ENSP00000586577.1

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102308 AN: 151952 Hom.: 35172 Cov.: 33

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.673 AC: 102397 AN: 152070 Hom.: 35208 Cov.: 33 AF XY: 0.667 AC XY: 49619 AN XY: 74344

African (AFR) AF: 0.810 AC: 33632 AN: 41506

American (AMR) AF: 0.573 AC: 8754 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1684 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2335 AN: 5176

South Asian (SAS) AF: 0.534 AC: 2573 AN: 4818

European-Finnish (FIN) AF: 0.666 AC: 7027 AN: 10556

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44335 AN: 67966

Other (OTH) AF: 0.630 AC: 1329 AN: 2110

Alfa AF: 0.674 Hom.: 4105

Bravo AF: 0.668

Asia WGS AF: 0.547 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.50
PhyloP100		0.80
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: rs1170169; hg19: chr13-42697807;