chrX-50386465-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001013742.4(DGKK):c.2240C>A(p.Pro747His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000024 in 1,209,049 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 10 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGKK | NM_001013742.4 | c.2240C>A | p.Pro747His | missense_variant | 15/28 | ENST00000611977.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGKK | ENST00000611977.2 | c.2240C>A | p.Pro747His | missense_variant | 15/28 | 1 | NM_001013742.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000897 AC: 1AN: 111466Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33636
GnomAD3 exomes AF: 0.0000386 AC: 7AN: 181224Hom.: 0 AF XY: 0.0000446 AC XY: 3AN XY: 67320
GnomAD4 exome AF: 0.0000255 AC: 28AN: 1097583Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 10AN XY: 363105
GnomAD4 genome ? AF: 0.00000897 AC: 1AN: 111466Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33636
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.2240C>A (p.P747H) alteration is located in exon 15 (coding exon 15) of the DGKK gene. This alteration results from a C to A substitution at nucleotide position 2240, causing the proline (P) at amino acid position 747 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