13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTT

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_623-2insTTTTTTTTTTTTTTTTTTTTTTTTTT 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 0.00049 (11 hom., cov: 0)
  • Exomes 𝑓: 0.0011 (57 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-CTTTTTTTTTTTTTTTTTTTTTTTTTT is Benign according to our data. Variant chr13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTT is described in ClinVar as [Likely_benign]. Clinvar id is 2643784.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd at 31 AD gene.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.000489 AC: 31 AN: 63404 Hom.: 11 Cov.: 0

Gnomad AFR AF: 0.000157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000528

Gnomad ASJ AF: 0.00104

Gnomad EAS AF: 0.000994

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000664

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00106 AC: 161 AN: 152086 Hom.: 57 Cov.: 15 AF XY: 0.000979 AC XY: 80 AN XY: 81696

Gnomad4 AFR exome AF: 0.00110

Gnomad4 AMR exome AF: 0.000553

Gnomad4 ASJ exome AF: 0.00114

Gnomad4 EAS exome AF: 0.000419

Gnomad4 SAS exome AF: 0.000466

Gnomad4 FIN exome AF: 0.000706

Gnomad4 NFE exome AF: 0.00130

Gnomad4 OTH exome AF: 0.00129

GnomAD4 genome AF: 0.000489 AC: 31 AN: 63400 Hom.: 11 Cov.: 0 AF XY: 0.000575 AC XY: 16 AN XY: 27844

Gnomad4 AFR AF: 0.000157

Gnomad4 AMR AF: 0.000528

Gnomad4 ASJ AF: 0.00104

Gnomad4 EAS AF: 0.000996

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000664

Gnomad4 OTH AF: 0.00

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

Dec 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;