rs9315897

Variant names:

• chr13-42164846-T-C
• rs9315897
• NM_178009.5:c.856-485T>C

Variant summary

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

The NM_178009.5(DGKH):​c.856-485T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,186 control chromosomes in the GnomAD database, including 1,497 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 0.13 (1497 hom., cov: 32)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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 (SAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKH	NM_178009.5	c.856-485T>C		intron_variant	Intron 7 of 29	ENST00000337343.9	NP_821077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKH	ENST00000337343.9	c.856-485T>C		intron_variant	Intron 7 of 29	1	NM_178009.5	ENSP00000337572.4

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19659 AN: 152068 Hom.: 1496 Cov.: 32

Gnomad AFR AF: 0.0705

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0861

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.129 AC: 19677 AN: 152186 Hom.: 1497 Cov.: 32 AF XY: 0.128 AC XY: 9552 AN XY: 74412

Gnomad4 AFR AF: 0.0707

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0861

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.176

Alfa AF: 0.153 Hom.: 863

Bravo AF: 0.130

Asia WGS AF: 0.130 AC: 454 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	1.2
DANN	Benign	0.65

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: rs9315897; hg19: chr13-42738982;