chr13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
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
NM_178009.5 intron
Scores
Not classified
Clinical Significance
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
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: 100AN: 63400Hom.: 33 Cov.: 0
GnomAD3 genomes
?
AF:
AC:
100
AN:
63400
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000907 AC: 138AN: 152094Hom.: 50 Cov.: 15 AF XY: 0.00103 AC XY: 84AN XY: 81706
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
138
AN:
152094
Hom.:
Cov.:
15
AF XY:
AC XY:
84
AN XY:
81706
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00158 AC: 100AN: 63396Hom.: 33 Cov.: 0 AF XY: 0.00172 AC XY: 48AN XY: 27842
GnomAD4 genome
?
AF:
AC:
100
AN:
63396
Hom.:
Cov.:
0
AF XY:
AC XY:
48
AN XY:
27842
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
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:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at