13-42159244-C-CTTTTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_178009.5(DGKH):c.623-3_623-2insTTTTTTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0021 (42 hom., cov: 0)
  • Exomes 𝑓: 0.0028 (145 hom.)
  • Failed GnomAD Quality Control
• Consequence: DGKH NM_178009.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0540

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 13-42159244-C-CTTTTTTTTTTTTTTTTTTTT is Benign according to our data. Variant chr13-42159244-C-CTTTTTTTTTTTTTTTTTTTT is described in ClinVar as [Likely_benign]. Clinvar id is 2643783.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd at 135 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKH	NM_178009.5	c.623-3_623-2insTTTTTTTTTTTTTTTTTTTT		intron_variant		ENST00000337343.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKH	ENST00000337343.9	c.623-3_623-2insTTTTTTTTTTTTTTTTTTTT		intron_variant		1	NM_178009.5	P1

Frequencies

GnomAD3 genomes AF: 0.00213 AC: 135 AN: 63398 Hom.: 42 Cov.: 0

Gnomad AFR AF: 0.00168

Gnomad AMI AF: 0.00211

Gnomad AMR AF: 0.00422

Gnomad ASJ AF: 0.000521

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00250

Gnomad OTH AF: 0.00252

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00277 AC: 421 AN: 152064 Hom.: 145 Cov.: 15 AF XY: 0.00249 AC XY: 203 AN XY: 81688

Gnomad4 AFR exome AF: 0.00151

Gnomad4 AMR exome AF: 0.00350

Gnomad4 ASJ exome AF: 0.00227

Gnomad4 EAS exome AF: 0.00346

Gnomad4 SAS exome AF: 0.00252

Gnomad4 FIN exome AF: 0.00159

Gnomad4 NFE exome AF: 0.00292

Gnomad4 OTH exome AF: 0.00232

GnomAD4 genome AF: 0.00213 AC: 135 AN: 63394 Hom.: 42 Cov.: 0 AF XY: 0.00183 AC XY: 51 AN XY: 27844

Gnomad4 AFR AF: 0.00167

Gnomad4 AMR AF: 0.00422

Gnomad4 ASJ AF: 0.000521

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00250

Gnomad4 OTH AF: 0.00252

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

DGKH: BS2 -

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: rs57531279; hg19: chr13-42733380;