rs6561030

Positions:

• chr13-42057583-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178009.5(DGKH):​c.192+8618C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,110 control chromosomes in the GnomAD database, including 2,524 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 0.18 (2524 hom., cov: 32)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DGKH	NM_178009.5	c.192+8618C>A		intron_variant		ENST00000337343.9	NP_821077.1
DGKH	NM_001204504.3	c.192+8618C>A		intron_variant			NP_001191433.1
DGKH	NM_152910.6	c.192+8618C>A		intron_variant			NP_690874.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DGKH	ENST00000337343.9	c.192+8618C>A		intron_variant		1	NM_178009.5	ENSP00000337572.4
DGKH	ENST00000261491.9	c.192+8618C>A		intron_variant		1		ENSP00000261491.4
DGKH	ENST00000379274.6	c.192+8618C>A		intron_variant		2		ENSP00000368576.3
DGKH	ENST00000611224.1	c.145-8508C>A		intron_variant		2		ENSP00000482250.1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26699 AN: 151990 Hom.: 2520 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.176 AC: 26719 AN: 152110 Hom.: 2524 Cov.: 32 AF XY: 0.178 AC XY: 13201 AN XY: 74366

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.192

Alfa AF: 0.158 Hom.: 3121

Bravo AF: 0.174

Asia WGS AF: 0.293 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs6561030; hg19: chr13-42631719;