rs2295553
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_023935.3(DDRGK1):c.92-72G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,433,712 control chromosomes in the GnomAD database, including 191,646 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.53 ( 21764 hom., cov: 33)
Exomes 𝑓: 0.51 ( 169882 hom. )
Consequence
DDRGK1
NM_023935.3 intron
NM_023935.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.101
Genes affected
DDRGK1 (HGNC:16110): (DDRGK domain containing 1) The protein encoded by this gene interacts with components of the ubiquitin fold modifier 1 conjugation pathway and helps prevent apoptosis in ER-stressed secretory tissues. In addition, the encoded protein regulates nuclear factor-κB activity. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDRGK1 | NM_023935.3 | c.92-72G>A | intron_variant | ENST00000354488.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDRGK1 | ENST00000354488.8 | c.92-72G>A | intron_variant | 1 | NM_023935.3 | P1 | |||
DDRGK1 | ENST00000380201.2 | c.92-72G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.530 AC: 80556AN: 152036Hom.: 21735 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.513 AC: 657107AN: 1281558Hom.: 169882 AF XY: 0.511 AC XY: 317546AN XY: 620820
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GnomAD4 genome ? AF: 0.530 AC: 80627AN: 152154Hom.: 21764 Cov.: 33 AF XY: 0.523 AC XY: 38898AN XY: 74370
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at