13-42062807-T-C

Variant names:

• chr13-42062807-T-C
• rs943390
• NM_178009.5:c.192+13842T>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.192+13842T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,154 control chromosomes in the GnomAD database, including 32,696 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 0.65 (32696 hom., cov: 33)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 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.192+13842T>C		intron	N/A	NP_821077.1	Q86XP1-1
	DGKH	NM_001204504.3		c.192+13842T>C		intron	N/A	NP_001191433.1	Q86XP1-2
	DGKH	NM_152910.6		c.192+13842T>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.192+13842T>C		intron	N/A	ENSP00000337572.4	Q86XP1-1
	DGKH	ENST00000261491.9	TSL:1	c.192+13842T>C		intron	N/A	ENSP00000261491.4	Q86XP1-2
	DGKH	ENST00000916518.1		c.192+13842T>C		intron	N/A	ENSP00000586577.1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98843 AN: 152036 Hom.: 32670 Cov.: 33

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.650 AC: 98903 AN: 152154 Hom.: 32696 Cov.: 33 AF XY: 0.656 AC XY: 48814 AN XY: 74378

African (AFR) AF: 0.602 AC: 24984 AN: 41480

American (AMR) AF: 0.784 AC: 12001 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2303 AN: 3472

East Asian (EAS) AF: 0.964 AC: 4996 AN: 5182

South Asian (SAS) AF: 0.768 AC: 3702 AN: 4820

European-Finnish (FIN) AF: 0.580 AC: 6139 AN: 10580

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42487 AN: 68000

Other (OTH) AF: 0.687 AC: 1450 AN: 2110

Alfa AF: 0.644 Hom.: 94723

Bravo AF: 0.664

Asia WGS AF: 0.813 AC: 2824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		-0.76
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: rs943390; hg19: chr13-42636943; COSMIC: COSV54939958;