2-233437387-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152879.3(DGKD):c.830C>T(p.Ser277Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,614,116 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 (★).
Frequency
Consequence
NM_152879.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGKD | NM_152879.3 | c.830C>T | p.Ser277Leu | missense_variant | 8/30 | ENST00000264057.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGKD | ENST00000264057.7 | c.830C>T | p.Ser277Leu | missense_variant | 8/30 | 1 | NM_152879.3 | ||
DGKD | ENST00000409813.7 | c.698C>T | p.Ser233Leu | missense_variant | 7/29 | 1 | P1 | ||
DGKD | ENST00000490764.5 | n.663C>T | non_coding_transcript_exon_variant | 6/19 | 1 | ||||
DGKD | ENST00000474488.1 | n.395C>T | non_coding_transcript_exon_variant | 5/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251404Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135878
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461808Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727212
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2023 | The c.830C>T (p.S277L) alteration is located in exon 8 (coding exon 8) of the DGKD gene. This alteration results from a C to T substitution at nucleotide position 830, causing the serine (S) at amino acid position 277 to be replaced by a leucine (L). 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