chr4-961519-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001347.4(DGKQ):c.2522G>A(p.Arg841His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000994 in 1,609,118 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.2522G>A | p.Arg841His | missense_variant | Exon 21 of 23 | ENST00000273814.8 | NP_001338.2 | |
DGKQ | XM_047449687.1 | c.2609G>A | p.Arg870His | missense_variant | Exon 21 of 23 | XP_047305643.1 | ||
DGKQ | XM_011513411.2 | c.2522G>A | p.Arg841His | missense_variant | Exon 21 of 23 | XP_011511713.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DGKQ | ENST00000273814.8 | c.2522G>A | p.Arg841His | missense_variant | Exon 21 of 23 | 1 | NM_001347.4 | ENSP00000273814.3 | ||
DGKQ | ENST00000509465.5 | c.2321G>A | p.Arg774His | missense_variant | Exon 20 of 22 | 5 | ENSP00000425862.1 | |||
DGKQ | ENST00000515182.1 | c.167G>A | p.Arg56His | missense_variant | Exon 3 of 5 | 5 | ENSP00000421756.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000426 AC: 1AN: 234498Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 128606
GnomAD4 exome AF: 0.00000961 AC: 14AN: 1456930Hom.: 0 Cov.: 34 AF XY: 0.00000690 AC XY: 5AN XY: 724708
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2522G>A (p.R841H) alteration is located in exon 21 (coding exon 21) of the DGKQ gene. This alteration results from a G to A substitution at nucleotide position 2522, causing the arginine (R) at amino acid position 841 to be replaced by a histidine (H). 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