13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

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_623-2insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 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 0.0026 (52 hom., cov: 0)
  • Exomes 𝑓: 0.0011 (58 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-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT is Benign according to our data. Variant chr13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT is described in ClinVar as [Likely_benign]. Clinvar id is 2643785.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd at 167 AD gene.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00263 AC: 167 AN: 63402 Hom.: 52 Cov.: 0

Gnomad AFR AF: 0.00152

Gnomad AMI AF: 0.0105

Gnomad AMR AF: 0.00317

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00149

Gnomad SAS AF: 0.00232

Gnomad FIN AF: 0.00538

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00332

Gnomad OTH AF: 0.00252

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00105 AC: 160 AN: 152094 Hom.: 58 Cov.: 15 AF XY: 0.00110 AC XY: 90 AN XY: 81704

Gnomad4 AFR exome AF: 0.000138

Gnomad4 AMR exome AF: 0.000737

Gnomad4 ASJ exome AF: 0.000568

Gnomad4 EAS exome AF: 0.000733

Gnomad4 SAS exome AF: 0.000513

Gnomad4 FIN exome AF: 0.00229

Gnomad4 NFE exome AF: 0.00122

Gnomad4 OTH exome AF: 0.00116

GnomAD4 genome AF: 0.00263 AC: 167 AN: 63398 Hom.: 52 Cov.: 0 AF XY: 0.00277 AC XY: 77 AN XY: 27846

Gnomad4 AFR AF: 0.00152

Gnomad4 AMR AF: 0.00317

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00149

Gnomad4 SAS AF: 0.00233

Gnomad4 FIN AF: 0.00538

Gnomad4 NFE AF: 0.00332

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

Mar 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;