4-961812-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001347.4(DGKQ):c.2338G>A(p.Val780Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000125 in 1,605,146 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001347.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DGKQ | NM_001347.4 | c.2338G>A | p.Val780Met | missense_variant | Exon 20 of 23 | ENST00000273814.8 | NP_001338.2 | |
DGKQ | XM_047449687.1 | c.2425G>A | p.Val809Met | missense_variant | Exon 20 of 23 | XP_047305643.1 | ||
DGKQ | XM_011513411.2 | c.2338G>A | p.Val780Met | missense_variant | Exon 20 of 23 | XP_011511713.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DGKQ | ENST00000273814.8 | c.2338G>A | p.Val780Met | missense_variant | Exon 20 of 23 | 1 | NM_001347.4 | ENSP00000273814.3 | ||
DGKQ | ENST00000509465.5 | c.2137G>A | p.Val713Met | missense_variant | Exon 19 of 22 | 5 | ENSP00000425862.1 | |||
DGKQ | ENST00000515182.1 | c.107+170G>A | intron_variant | Intron 2 of 4 | 5 | ENSP00000421756.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000330 AC: 8AN: 242156Hom.: 0 AF XY: 0.0000306 AC XY: 4AN XY: 130826
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1452874Hom.: 0 Cov.: 34 AF XY: 0.0000125 AC XY: 9AN XY: 722320
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2338G>A (p.V780M) alteration is located in exon 20 (coding exon 20) of the DGKQ gene. This alteration results from a G to A substitution at nucleotide position 2338, causing the valine (V) at amino acid position 780 to be replaced by a methionine (M). 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