13-42094549-A-G

Variant names:

• chr13-42094549-A-G
• rs1170195
• NM_178009.5:c.193-32914A>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.193-32914A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,054 control chromosomes in the GnomAD database, including 12,575 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 0.40 (12575 hom., cov: 32)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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.193-32914A>G		intron	N/A	NP_821077.1	Q86XP1-1
	DGKH	NM_001204504.3		c.193-32914A>G		intron	N/A	NP_001191433.1	Q86XP1-2
	DGKH	NM_152910.6		c.193-32914A>G		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.193-32914A>G		intron	N/A	ENSP00000337572.4	Q86XP1-1
	DGKH	ENST00000261491.9	TSL:1	c.193-32914A>G		intron	N/A	ENSP00000261491.4	Q86XP1-2
	DGKH	ENST00000916518.1		c.193-32914A>G		intron	N/A	ENSP00000586577.1

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60233 AN: 151936 Hom.: 12552 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.397 AC: 60316 AN: 152054 Hom.: 12575 Cov.: 32 AF XY: 0.397 AC XY: 29497 AN XY: 74328

African (AFR) AF: 0.511 AC: 21198 AN: 41466

American (AMR) AF: 0.436 AC: 6661 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1268 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1004 AN: 5184

South Asian (SAS) AF: 0.429 AC: 2059 AN: 4800

European-Finnish (FIN) AF: 0.288 AC: 3039 AN: 10568

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23834 AN: 67982

Other (OTH) AF: 0.397 AC: 838 AN: 2112

Alfa AF: 0.369 Hom.: 17670

Bravo AF: 0.411

Asia WGS AF: 0.335 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.27
PhyloP100		-1.2
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: rs1170195; hg19: chr13-42668685;