chrX-50378589-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_001013742.4(DGKK):c.2965C>T(p.Arg989Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000247 in 1,092,471 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001013742.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGKK | NM_001013742.4 | c.2965C>T | p.Arg989Cys | missense_variant | 21/28 | ENST00000611977.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGKK | ENST00000611977.2 | c.2965C>T | p.Arg989Cys | missense_variant | 21/28 | 1 | NM_001013742.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 exomes AF: 0.00000590 AC: 1AN: 169465Hom.: 0 AF XY: 0.0000176 AC XY: 1AN XY: 56941
GnomAD4 exome AF: 0.0000247 AC: 27AN: 1092471Hom.: 0 Cov.: 30 AF XY: 0.0000251 AC XY: 9AN XY: 358637
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.2965C>T (p.R989C) alteration is located in exon 21 (coding exon 21) of the DGKK gene. This alteration results from a C to T substitution at nucleotide position 2965, causing the arginine (R) at amino acid position 989 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