rs9525580

Variant names:

• chr13-42146563-G-A
• rs9525580
• NM_178009.5:c.385-8728G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-42146563-G-A
• chr13-42146563-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178009.5(DGKH):​c.385-8728G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,132 control chromosomes in the GnomAD database, including 4,363 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 0.23 (4363 hom., cov: 32)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• Publications: 10 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKH	NM_178009.5	c.385-8728G>A		intron_variant	Intron 3 of 29	ENST00000337343.9	NP_821077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKH	ENST00000337343.9	c.385-8728G>A		intron_variant	Intron 3 of 29	1	NM_178009.5	ENSP00000337572.4

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35208 AN: 152014 Hom.: 4359 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.232 AC: 35236 AN: 152132 Hom.: 4363 Cov.: 32 AF XY: 0.230 AC XY: 17106 AN XY: 74384

African (AFR) AF: 0.171 AC: 7109 AN: 41516

American (AMR) AF: 0.219 AC: 3346 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1126 AN: 3472

East Asian (EAS) AF: 0.121 AC: 626 AN: 5186

South Asian (SAS) AF: 0.288 AC: 1388 AN: 4824

European-Finnish (FIN) AF: 0.211 AC: 2234 AN: 10572

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18529 AN: 67966

Other (OTH) AF: 0.273 AC: 575 AN: 2110

Alfa AF: 0.236 Hom.: 734

Bravo AF: 0.230

Asia WGS AF: 0.190 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.71
DANN	Benign	0.49
PhyloP100		-0.92
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: rs9525580; hg19: chr13-42720699;