chr4-961784-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001347.4(DGKQ):āc.2366A>Gā(p.His789Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000168 in 1,610,508 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001347.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DGKQ | NM_001347.4 | c.2366A>G | p.His789Arg | missense_variant | 20/23 | ENST00000273814.8 | NP_001338.2 | |
DGKQ | XM_047449687.1 | c.2453A>G | p.His818Arg | missense_variant | 20/23 | XP_047305643.1 | ||
DGKQ | XM_011513411.2 | c.2366A>G | p.His789Arg | missense_variant | 20/23 | XP_011511713.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DGKQ | ENST00000273814.8 | c.2366A>G | p.His789Arg | missense_variant | 20/23 | 1 | NM_001347.4 | ENSP00000273814 | P1 | |
DGKQ | ENST00000509465.5 | c.2168A>G | p.His723Arg | missense_variant | 19/22 | 5 | ENSP00000425862 | |||
DGKQ | ENST00000515182.1 | c.107+198A>G | intron_variant | 5 | ENSP00000421756 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151890Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 247610Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134030
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1458618Hom.: 0 Cov.: 34 AF XY: 0.0000138 AC XY: 10AN XY: 725596
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151890Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74178
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.2366A>G (p.H789R) alteration is located in exon 20 (coding exon 20) of the DGKQ gene. This alteration results from a A to G substitution at nucleotide position 2366, causing the histidine (H) at amino acid position 789 to be replaced by an arginine (R). 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