X-50380019-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001013742.4(DGKK):c.2716C>T(p.Arg906Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000174 in 1,209,966 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R906H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001013742.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGKK | NM_001013742.4 | c.2716C>T | p.Arg906Cys | missense_variant | 19/28 | ENST00000611977.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGKK | ENST00000611977.2 | c.2716C>T | p.Arg906Cys | missense_variant | 19/28 | 1 | NM_001013742.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112076Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34226
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 181182Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67324
GnomAD4 exome AF: 0.0000173 AC: 19AN: 1097835Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 6AN XY: 363305
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112131Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34291
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.2716C>T (p.R906C) alteration is located in exon 19 (coding exon 19) of the DGKK gene. This alteration results from a C to T substitution at nucleotide position 2716, causing the arginine (R) at amino acid position 906 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at