chr4-961469-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001347.4(DGKQ):āc.2572A>Gā(p.Met858Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000978 in 1,595,058 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001347.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DGKQ | NM_001347.4 | c.2572A>G | p.Met858Val | missense_variant, splice_region_variant | 21/23 | ENST00000273814.8 | NP_001338.2 | |
DGKQ | XM_047449687.1 | c.2659A>G | p.Met887Val | missense_variant, splice_region_variant | 21/23 | XP_047305643.1 | ||
DGKQ | XM_011513411.2 | c.2572A>G | p.Met858Val | missense_variant, splice_region_variant | 21/23 | XP_011511713.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DGKQ | ENST00000273814.8 | c.2572A>G | p.Met858Val | missense_variant, splice_region_variant | 21/23 | 1 | NM_001347.4 | ENSP00000273814 | P1 | |
DGKQ | ENST00000509465.5 | c.2374A>G | p.Met792Val | missense_variant, splice_region_variant | 20/22 | 5 | ENSP00000425862 | |||
DGKQ | ENST00000515182.1 | c.217A>G | p.Met73Val | missense_variant, splice_region_variant | 3/5 | 5 | ENSP00000421756 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 152000Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000189 AC: 40AN: 211482Hom.: 0 AF XY: 0.000172 AC XY: 20AN XY: 116616
GnomAD4 exome AF: 0.000100 AC: 145AN: 1443058Hom.: 0 Cov.: 33 AF XY: 0.000105 AC XY: 75AN XY: 716992
GnomAD4 genome AF: 0.0000724 AC: 11AN: 152000Hom.: 0 Cov.: 33 AF XY: 0.0000943 AC XY: 7AN XY: 74250
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 28, 2022 | The c.2572A>G (p.M858V) alteration is located in exon 21 (coding exon 21) of the DGKQ gene. This alteration results from a A to G substitution at nucleotide position 2572, causing the methionine (M) at amino acid position 858 to be replaced by a valine (V). 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