rs2067373

chr13-42124309-A-ATTATAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_178009.5(DGKH):c.193-3153_193-3152insTATATT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 151,890 control chromosomes in the GnomAD database, including 35,121 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (35121 hom., cov: 0)
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKH	NM_178009.5	c.193-3153_193-3152insTATATT		intron_variant		ENST00000337343.9
DGKH	NM_001204504.3	c.193-3153_193-3152insTATATT		intron_variant
DGKH	NM_152910.6	c.193-3153_193-3152insTATATT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKH	ENST00000337343.9	c.193-3153_193-3152insTATATT		intron_variant		1	NM_178009.5	P1
DGKH	ENST00000261491.9	c.193-3153_193-3152insTATATT		intron_variant		1
DGKH	ENST00000379274.6	c.193-3153_193-3152insTATATT		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102115 AN: 151772 Hom.: 35085 Cov.: 0

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.673 AC: 102204 AN: 151890 Hom.: 35121 Cov.: 0 AF XY: 0.667 AC XY: 49523 AN XY: 74242

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.628

Alfa AF: 0.680 Hom.: 3774

Asia WGS AF: 0.544 AC: 1885 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2067373; hg19: chr13-42698445;