chr17-56843797-C-CAAAAAAAA

Variant names:

• chr17-56843797-C-CAAAAAAAA
• rs368992473
• NM_003647.3:c.465-212_465-205dupAAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_003647.3(DGKE):​c.465-212_465-205dupAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.00033 (1 hom., cov: 0)
• Consequence: DGKE NM_003647.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

Genes affected

DGKE (HGNC:2852): (diacylglycerol kinase epsilon) Diacylglycerol kinases are thought to be involved mainly in the regeneration of phosphatidylinositol (PI) from diacylglycerol in the PI-cycle during cell signal transduction. When expressed in mammalian cells, DGK-epsilon shows specificity for arachidonyl-containing diacylglycerol. DGK-epsilon is expressed predominantly in testis. [provided by RefSeq, Jul 2008]

TRIM25 (HGNC:12932): (tripartite motif containing 25) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein is an RNA binding protein, functions as a ubiquitin E3 ligase and is involved in multiple cellular processes, including regulation of antiviral innate immunity. [provided by RefSeq, Sep 2021]

LOC124904036 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000329 (36/109274) while in subpopulation NFE AF= 0.000536 (29/54122). AF 95% confidence interval is 0.000382. There are 1 homozygotes in gnomad4. There are 12 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKE	NM_003647.3	c.465-212_465-205dupAAAAAAAA		intron_variant	Intron 2 of 11	ENST00000284061.8	NP_003638.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKE	ENST00000284061.8	c.465-222_465-221insAAAAAAAA		intron_variant	Intron 2 of 11	1	NM_003647.3	ENSP00000284061.3

Frequencies

GnomAD3 genomes AF: 0.000329 AC: 36 AN: 109274 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.0000345

Gnomad AMI AF: 0.00134

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000254

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000983

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000536

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000329 AC: 36 AN: 109274 Hom.: 1 Cov.: 0 AF XY: 0.000237 AC XY: 12 AN XY: 50722

Gnomad4 AFR AF: 0.0000344

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000255

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000983

Gnomad4 NFE AF: 0.000536

Gnomad4 OTH AF: 0.00

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: rs368992473; hg19: chr17-54921158;