rs9315885

Variant names:

• chr13-42068674-C-T
• rs9315885
• NM_178009.5:c.192+19709C>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.192+19709C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 151,932 control chromosomes in the GnomAD database, including 29,720 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 0.62 (29720 hom., cov: 32)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359
• 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]

MAPK6P3 (HGNC:18977): (mitogen-activated protein kinase 6 pseudogene 3)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKH	NM_178009.5	c.192+19709C>T		intron_variant	Intron 1 of 29	ENST00000337343.9	NP_821077.1
MAPK6P3		n.42068674C>T		intragenic_variant
DGKH	NM_001204504.3	c.192+19709C>T		intron_variant	Intron 2 of 29		NP_001191433.1
DGKH	NM_152910.6	c.192+19709C>T		intron_variant	Intron 1 of 28		NP_690874.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKH	ENST00000337343.9	c.192+19709C>T		intron_variant	Intron 1 of 29	1	NM_178009.5	ENSP00000337572.4
DGKH	ENST00000261491.9	c.192+19709C>T		intron_variant	Intron 1 of 28	1		ENSP00000261491.4
DGKH	ENST00000379274.6	c.192+19709C>T		intron_variant	Intron 2 of 29	2		ENSP00000368576.3

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94485 AN: 151814 Hom.: 29692 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.622 AC: 94549 AN: 151932 Hom.: 29720 Cov.: 32 AF XY: 0.618 AC XY: 45903 AN XY: 74236

African (AFR) AF: 0.569 AC: 23572 AN: 41414

American (AMR) AF: 0.587 AC: 8943 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1700 AN: 3464

East Asian (EAS) AF: 0.523 AC: 2708 AN: 5178

South Asian (SAS) AF: 0.617 AC: 2975 AN: 4820

European-Finnish (FIN) AF: 0.630 AC: 6649 AN: 10548

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45973 AN: 67952

Other (OTH) AF: 0.604 AC: 1273 AN: 2106

Alfa AF: 0.648 Hom.: 6054

Bravo AF: 0.612

Asia WGS AF: 0.585 AC: 2036 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.7
DANN	Benign	0.61
PhyloP100		0.36
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: rs9315885; hg19: chr13-42642810;