chr13-42134315-A-G

Position:

• chr13-42134315-A-G

Variant summary

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

The NM_178009.5(DGKH):​c.384+4683A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,054 control chromosomes in the GnomAD database, including 11,327 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 0.37 (11327 hom., cov: 32)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKH	NM_178009.5	c.384+4683A>G		intron_variant		ENST00000337343.9
DGKH	NM_001204504.3	c.384+4683A>G		intron_variant
DGKH	NM_152910.6	c.384+4683A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKH	ENST00000337343.9	c.384+4683A>G		intron_variant		1	NM_178009.5	P1
DGKH	ENST00000261491.9	c.384+4683A>G		intron_variant		1
DGKH	ENST00000379274.6	c.384+4683A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56884 AN: 151936 Hom.: 11309 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.375 AC: 56950 AN: 152054 Hom.: 11327 Cov.: 32 AF XY: 0.376 AC XY: 27919 AN XY: 74326

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.396

Alfa AF: 0.410 Hom.: 3555

Bravo AF: 0.372

Asia WGS AF: 0.311 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.011
DANN	Benign	0.35

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: rs994856; hg19: chr13-42708451;