13-42079301-C-A

Variant names:

• chr13-42079301-C-A
• rs1012053
• NM_178009.5:c.192+30336C>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.192+30336C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 152,090 control chromosomes in the GnomAD database, including 54,014 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 0.84 (54014 hom., cov: 30)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 41 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKH	NM_178009.5	c.192+30336C>A		intron_variant	Intron 1 of 29	ENST00000337343.9	NP_821077.1
DGKH	NM_001204504.3	c.192+30336C>A		intron_variant	Intron 2 of 29		NP_001191433.1
DGKH	NM_152910.6	c.192+30336C>A		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.192+30336C>A		intron_variant	Intron 1 of 29	1	NM_178009.5	ENSP00000337572.4
DGKH	ENST00000261491.9	c.192+30336C>A		intron_variant	Intron 1 of 28	1		ENSP00000261491.4
DGKH	ENST00000379274.6	c.192+30336C>A		intron_variant	Intron 2 of 29	2		ENSP00000368576.3

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127447 AN: 151972 Hom.: 53957 Cov.: 30

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.839 AC: 127564 AN: 152090 Hom.: 54014 Cov.: 30 AF XY: 0.832 AC XY: 61872 AN XY: 74336

African (AFR) AF: 0.925 AC: 38410 AN: 41504

American (AMR) AF: 0.755 AC: 11550 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2481 AN: 3468

East Asian (EAS) AF: 0.550 AC: 2842 AN: 5164

South Asian (SAS) AF: 0.742 AC: 3566 AN: 4806

European-Finnish (FIN) AF: 0.795 AC: 8411 AN: 10576

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57616 AN: 67970

Other (OTH) AF: 0.828 AC: 1750 AN: 2114

Alfa AF: 0.831 Hom.: 221741

Bravo AF: 0.834

Asia WGS AF: 0.695 AC: 2414 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.090
PhyloP100		-2.4
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: rs1012053; hg19: chr13-42653437;