13-42115924-C-T

Position:

• chr13-42115924-C-T

Variant summary

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

The NM_178009.5(DGKH):​c.193-11539C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,878 control chromosomes in the GnomAD database, including 14,776 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 0.44 (14776 hom., cov: 32)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DGKH	NM_178009.5	c.193-11539C>T		intron_variant		ENST00000337343.9	NP_821077.1
DGKH	NM_001204504.3	c.193-11539C>T		intron_variant			NP_001191433.1
DGKH	NM_152910.6	c.193-11539C>T		intron_variant			NP_690874.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DGKH	ENST00000337343.9	c.193-11539C>T		intron_variant		1	NM_178009.5	ENSP00000337572.4
DGKH	ENST00000261491.9	c.193-11539C>T		intron_variant		1		ENSP00000261491.4
DGKH	ENST00000379274.6	c.193-11539C>T		intron_variant		2		ENSP00000368576.3

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66337 AN: 151760 Hom.: 14769 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.437 AC: 66364 AN: 151878 Hom.: 14776 Cov.: 32 AF XY: 0.430 AC XY: 31913 AN XY: 74232

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.423

Alfa AF: 0.442 Hom.: 25492

Bravo AF: 0.421

Asia WGS AF: 0.401 AC: 1394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
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: rs7981733; hg19: chr13-42690060;