rs1177637

Variant names:

• chr13-42118687-G-A
• rs1177637
• NM_178009.5:c.193-8776G>A

Variant summary

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

The NM_178009.5(DGKH):​c.193-8776G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,184 control chromosomes in the GnomAD database, including 50,180 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 0.81 (50180 hom., cov: 32)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680
• Publications: 3 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 = 0.886 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKH	NM_178009.5	MANE Select	c.193-8776G>A		intron	N/A	NP_821077.1
	DGKH	NM_001204504.3		c.193-8776G>A		intron	N/A	NP_001191433.1
	DGKH	NM_152910.6		c.193-8776G>A		intron	N/A	NP_690874.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKH	ENST00000337343.9	TSL:1 MANE Select	c.193-8776G>A		intron	N/A	ENSP00000337572.4
	DGKH	ENST00000261491.9	TSL:1	c.193-8776G>A		intron	N/A	ENSP00000261491.4
	DGKH	ENST00000379274.6	TSL:2	c.193-8776G>A		intron	N/A	ENSP00000368576.3

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122820 AN: 152066 Hom.: 50126 Cov.: 32

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.808 AC: 122934 AN: 152184 Hom.: 50180 Cov.: 32 AF XY: 0.801 AC XY: 59584 AN XY: 74390

African (AFR) AF: 0.894 AC: 37135 AN: 41534

American (AMR) AF: 0.727 AC: 11114 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2283 AN: 3472

East Asian (EAS) AF: 0.539 AC: 2778 AN: 5156

South Asian (SAS) AF: 0.718 AC: 3456 AN: 4814

European-Finnish (FIN) AF: 0.763 AC: 8074 AN: 10584

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55494 AN: 68020

Other (OTH) AF: 0.805 AC: 1699 AN: 2110

Alfa AF: 0.800 Hom.: 22058

Bravo AF: 0.805

Asia WGS AF: 0.681 AC: 2369 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	0.074
DANN	Benign	0.44
PhyloP100		-0.68
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: rs1177637; hg19: chr13-42692823;