rs2067373

Variant names:

• chr13-42124309-A-ATTATAT
• rs2067373
• NM_178009.5:c.193-3153_193-3152insTATATT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_178009.5(DGKH):​c.193-3153_193-3152insTATATT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (35121 hom., cov: 0)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659
• Publications: 2 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKH	NM_178009.5	c.193-3153_193-3152insTATATT		intron_variant	Intron 1 of 29	ENST00000337343.9	NP_821077.1
DGKH	NM_001204504.3	c.193-3153_193-3152insTATATT		intron_variant	Intron 2 of 29		NP_001191433.1
DGKH	NM_152910.6	c.193-3153_193-3152insTATATT		intron_variant	Intron 1 of 28		NP_690874.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKH	ENST00000337343.9	c.193-3154_193-3153insTTATAT		intron_variant	Intron 1 of 29	1	NM_178009.5	ENSP00000337572.4
DGKH	ENST00000261491.9	c.193-3154_193-3153insTTATAT		intron_variant	Intron 1 of 28	1		ENSP00000261491.4
DGKH	ENST00000379274.6	c.193-3154_193-3153insTTATAT		intron_variant	Intron 2 of 29	2		ENSP00000368576.3

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102115 AN: 151772 Hom.: 35085 Cov.: 0

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.673 AC: 102204 AN: 151890 Hom.: 35121 Cov.: 0 AF XY: 0.667 AC XY: 49523 AN XY: 74242

African (AFR) AF: 0.810 AC: 33545 AN: 41414

American (AMR) AF: 0.573 AC: 8748 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3468

East Asian (EAS) AF: 0.450 AC: 2329 AN: 5170

South Asian (SAS) AF: 0.533 AC: 2565 AN: 4808

European-Finnish (FIN) AF: 0.665 AC: 7005 AN: 10534

Middle Eastern (MID) AF: 0.586 AC: 170 AN: 290

European-Non Finnish (NFE) AF: 0.652 AC: 44280 AN: 67932

Other (OTH) AF: 0.628 AC: 1327 AN: 2112

Alfa AF: 0.680 Hom.: 3774

Asia WGS AF: 0.544 AC: 1885 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.66
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2067373; hg19: chr13-42698445;