13-42115924-C-T

Variant names:

• chr13-42115924-C-T
• rs7981733
• NM_178009.5:c.193-11539C>T

Variant summary

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

The NM_178009.5(DGKH):​c.193-11539C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,878 control chromosomes in the GnomAD database, including 14,776 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 0.44 (14776 hom., cov: 32)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.464 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.193-11539C>T		intron	N/A	NP_821077.1
	DGKH	NM_001204504.3		c.193-11539C>T		intron	N/A	NP_001191433.1
	DGKH	NM_152910.6		c.193-11539C>T		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.193-11539C>T		intron	N/A	ENSP00000337572.4
	DGKH	ENST00000261491.9	TSL:1	c.193-11539C>T		intron	N/A	ENSP00000261491.4
	DGKH	ENST00000916518.1		c.193-11539C>T		intron	N/A	ENSP00000586577.1

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66337 AN: 151760 Hom.: 14769 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.437 AC: 66364 AN: 151878 Hom.: 14776 Cov.: 32 AF XY: 0.430 AC XY: 31913 AN XY: 74232

African (AFR) AF: 0.452 AC: 18694 AN: 41392

American (AMR) AF: 0.298 AC: 4550 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1028 AN: 3472

East Asian (EAS) AF: 0.423 AC: 2183 AN: 5166

South Asian (SAS) AF: 0.305 AC: 1464 AN: 4802

European-Finnish (FIN) AF: 0.490 AC: 5155 AN: 10524

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31836 AN: 67934

Other (OTH) AF: 0.423 AC: 895 AN: 2116

Alfa AF: 0.446 Hom.: 58363

Bravo AF: 0.421

Asia WGS AF: 0.401 AC: 1394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.87
DANN	Benign	0.30
PhyloP100		-0.42
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: rs7981733; hg19: chr13-42690060;