rs312262696
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PM2PP3_StrongPP5_Moderate
The NM_003647.3(DGKE):c.889-1G>A variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,110 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_003647.3 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGKE | NM_003647.3 | c.889-1G>A | splice_acceptor_variant | ENST00000284061.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGKE | ENST00000284061.8 | c.889-1G>A | splice_acceptor_variant | 1 | NM_003647.3 | P1 | |||
DGKE | ENST00000572944.1 | c.719-1G>A | splice_acceptor_variant | 1 | |||||
TRIM25 | ENST00000648772.1 | c.*313+3248C>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461110Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726818
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Atypical hemolytic-uremic syndrome Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Richard Lifton Laboratory, Yale University School of Medicine | - | - - |
Immunoglobulin-mediated membranoproliferative glomerulonephritis Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München | Jun 07, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at