13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

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_623-2insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 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 0.0016 (33 hom., cov: 0)
  • Exomes 𝑓: 0.00091 (50 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-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT is Benign according to our data. Variant chr13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT is described in ClinVar as [Likely_benign]. Clinvar id is 2643788.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd at 100 AD gene.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00158 AC: 100 AN: 63400 Hom.: 33 Cov.: 0

Gnomad AFR AF: 0.000942

Gnomad AMI AF: 0.0105

Gnomad AMR AF: 0.00185

Gnomad ASJ AF: 0.00313

Gnomad EAS AF: 0.00398

Gnomad SAS AF: 0.00174

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00154

Gnomad OTH AF: 0.00252

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000907 AC: 138 AN: 152094 Hom.: 50 Cov.: 15 AF XY: 0.00103 AC XY: 84 AN XY: 81706

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00129

Gnomad4 ASJ exome AF: 0.000851

Gnomad4 EAS exome AF: 0.00168

Gnomad4 SAS exome AF: 0.000559

Gnomad4 FIN exome AF: 0.000706

Gnomad4 NFE exome AF: 0.000991

Gnomad4 OTH exome AF: 0.000774

GnomAD4 genome AF: 0.00158 AC: 100 AN: 63396 Hom.: 33 Cov.: 0 AF XY: 0.00172 AC XY: 48 AN XY: 27842

Gnomad4 AFR AF: 0.000942

Gnomad4 AMR AF: 0.00185

Gnomad4 ASJ AF: 0.00313

Gnomad4 EAS AF: 0.00398

Gnomad4 SAS AF: 0.00175

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00154

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

Jan 01, 2023

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;