13-42128575-C-T

Variant names:

• chr13-42128575-C-T
• rs1170155
• NM_178009.5:c.304-977C>T

Variant summary

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

The NM_178009.5(DGKH):​c.304-977C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,920 control chromosomes in the GnomAD database, including 31,402 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 0.64 (31402 hom., cov: 31)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.813
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKH	NM_178009.5	c.304-977C>T		intron_variant	Intron 2 of 29	ENST00000337343.9	NP_821077.1
DGKH	NM_001204504.3	c.304-977C>T		intron_variant	Intron 3 of 29		NP_001191433.1
DGKH	NM_152910.6	c.304-977C>T		intron_variant	Intron 2 of 28		NP_690874.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKH	ENST00000337343.9	c.304-977C>T		intron_variant	Intron 2 of 29	1	NM_178009.5	ENSP00000337572.4
DGKH	ENST00000261491.9	c.304-977C>T		intron_variant	Intron 2 of 28	1		ENSP00000261491.4
DGKH	ENST00000379274.6	c.304-977C>T		intron_variant	Intron 3 of 29	2		ENSP00000368576.3

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96918 AN: 151804 Hom.: 31386 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.638 AC: 96981 AN: 151920 Hom.: 31402 Cov.: 31 AF XY: 0.632 AC XY: 46929 AN XY: 74214

African (AFR) AF: 0.715 AC: 29613 AN: 41398

American (AMR) AF: 0.559 AC: 8531 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2120 AN: 5160

South Asian (SAS) AF: 0.525 AC: 2530 AN: 4816

European-Finnish (FIN) AF: 0.623 AC: 6561 AN: 10530

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.647 AC: 44008 AN: 67968

Other (OTH) AF: 0.602 AC: 1274 AN: 2116

Alfa AF: 0.630 Hom.: 95670

Bravo AF: 0.633

Asia WGS AF: 0.509 AC: 1771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.2
DANN	Benign	0.57
PhyloP100		0.81
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: rs1170155; hg19: chr13-42702711;