rs180870

Variant names:

• chr13-42219343-G-A
• rs180870
• NM_178009.5:c.3327G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-42219343-G-A
• chr13-42219343-G-C
• chr13-42219343-G-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_178009.5(DGKH):​c.3327G>A​(p.Glu1109Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 1,612,736 control chromosomes in the GnomAD database, including 358,502 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 0.65 (32614 hom., cov: 32)
  • Exomes 𝑓: 0.67 (325888 hom.)
• Consequence: DGKH NM_178009.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

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 -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BP7: Synonymous conserved (PhyloP=0.23 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKH	NM_178009.5	c.3327G>A	p.Glu1109Glu	synonymous_variant	Exon 27 of 30	ENST00000337343.9	NP_821077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKH	ENST00000337343.9	c.3327G>A	p.Glu1109Glu	synonymous_variant	Exon 27 of 30	1	NM_178009.5	ENSP00000337572.4

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99240 AN: 151944 Hom.: 32598 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.685

GnomAD3 exomes AF: 0.642 AC: 160810 AN: 250580 Hom.: 52491 AF XY: 0.638 AC XY: 86463 AN XY: 135428

Gnomad AFR exome AF: 0.616

Gnomad AMR exome AF: 0.573

Gnomad ASJ exome AF: 0.669

Gnomad EAS exome AF: 0.766

Gnomad SAS exome AF: 0.493

Gnomad FIN exome AF: 0.690

Gnomad NFE exome AF: 0.675

Gnomad OTH exome AF: 0.639

GnomAD4 exome AF: 0.666 AC: 972170 AN: 1460674 Hom.: 325888 Cov.: 45 AF XY: 0.661 AC XY: 480024 AN XY: 726712

Gnomad4 AFR exome AF: 0.614

Gnomad4 AMR exome AF: 0.576

Gnomad4 ASJ exome AF: 0.666

Gnomad4 EAS exome AF: 0.743

Gnomad4 SAS exome AF: 0.494

Gnomad4 FIN exome AF: 0.690

Gnomad4 NFE exome AF: 0.681

Gnomad4 OTH exome AF: 0.652

GnomAD4 genome AF: 0.653 AC: 99295 AN: 152062 Hom.: 32614 Cov.: 32 AF XY: 0.652 AC XY: 48409 AN XY: 74300

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.685

Alfa AF: 0.669 Hom.: 54998

Bravo AF: 0.653

Asia WGS AF: 0.627 AC: 2180 AN: 3478

EpiCase AF: 0.675

EpiControl AF: 0.670

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	5.8
DANN	Benign	0.58

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: rs180870; hg19: chr13-42793479; COSMIC: COSV54932190; COSMIC: COSV54932190;