chr13-42160253-C-G

Position:

• chr13-42160253-C-G

Variant summary

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

The NM_178009.5(DGKH):​c.855+117C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,354,792 control chromosomes in the GnomAD database, including 16,432 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 0.12 (1419 hom., cov: 32)
  • Exomes 𝑓: 0.15 (15013 hom.)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

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]

DGKH (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DGKH	NM_178009.5	c.855+117C>G		intron_variant		ENST00000337343.9	NP_821077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DGKH	ENST00000337343.9	c.855+117C>G		intron_variant		1	NM_178009.5	ENSP00000337572.4

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18244 AN: 152116 Hom.: 1418 Cov.: 32

Gnomad AFR AF: 0.0383

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.167

GnomAD4 exome AF: 0.153 AC: 184315 AN: 1202558 Hom.: 15013 AF XY: 0.154 AC XY: 93401 AN XY: 604570

Gnomad4 AFR exome AF: 0.0334

Gnomad4 AMR exome AF: 0.129

Gnomad4 ASJ exome AF: 0.174

Gnomad4 EAS exome AF: 0.0993

Gnomad4 SAS exome AF: 0.174

Gnomad4 FIN exome AF: 0.110

Gnomad4 NFE exome AF: 0.161

Gnomad4 OTH exome AF: 0.149

GnomAD4 genome AF: 0.120 AC: 18255 AN: 152234 Hom.: 1419 Cov.: 32 AF XY: 0.119 AC XY: 8868 AN XY: 74446

Gnomad4 AFR AF: 0.0385

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0866

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.169

Alfa AF: 0.0377 Hom.: 37

Bravo AF: 0.120

Asia WGS AF: 0.129 AC: 449 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	0.87
DANN	Benign	0.30

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: rs10492444; hg19: chr13-42734389; COSMIC: COSV54928078;