NM_178009.5:c.2036-897A>G

Variant names:

• chr13-42193988-A-G
• rs347391
• NM_178009.5:c.2036-897A>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.2036-897A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,220 control chromosomes in the GnomAD database, including 65,946 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 0.93 (65946 hom., cov: 32)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.962 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.2036-897A>G		intron	N/A	NP_821077.1
	DGKH	NM_001204504.3		c.2036-897A>G		intron	N/A	NP_001191433.1
	DGKH	NM_152910.6		c.2036-897A>G		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.2036-897A>G		intron	N/A	ENSP00000337572.4
	DGKH	ENST00000261491.9	TSL:1	c.2036-897A>G		intron	N/A	ENSP00000261491.4
	DGKH	ENST00000536612.3	TSL:1	c.1628-897A>G		intron	N/A	ENSP00000445114.2

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141317 AN: 152102 Hom.: 65903 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.986

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.929 AC: 141415 AN: 152220 Hom.: 65946 Cov.: 32 AF XY: 0.929 AC XY: 69178 AN XY: 74426

African (AFR) AF: 0.852 AC: 35345 AN: 41496

American (AMR) AF: 0.958 AC: 14659 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3191 AN: 3472

East Asian (EAS) AF: 0.905 AC: 4694 AN: 5186

South Asian (SAS) AF: 0.856 AC: 4123 AN: 4818

European-Finnish (FIN) AF: 0.986 AC: 10458 AN: 10610

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.968 AC: 65856 AN: 68022

Other (OTH) AF: 0.934 AC: 1973 AN: 2112

Alfa AF: 0.948 Hom.: 8503

Bravo AF: 0.928

Asia WGS AF: 0.853 AC: 2967 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	0.39
DANN	Benign	0.71
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: rs347391; hg19: chr13-42768124;