rs3813344
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001143676.3(SGK1):c.-368G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0794 in 206,858 control chromosomes in the GnomAD database, including 771 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 0.074 ( 490 hom., cov: 32)
Exomes 𝑓: 0.096 ( 281 hom. )
Consequence
SGK1
NM_001143676.3 5_prime_UTR
NM_001143676.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.284
Genes affected
SGK1 (HGNC:10810): (serum/glucocorticoid regulated kinase 1) This gene encodes a serine/threonine protein kinase that plays an important role in cellular stress response. This kinase activates certain potassium, sodium, and chloride channels, suggesting an involvement in the regulation of processes such as cell survival, neuronal excitability, and renal sodium excretion. High levels of expression of this gene may contribute to conditions such as hypertension and diabetic nephropathy. Several alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jan 2009]
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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 (NFE) allele frequency at 95% confidence interval = 0.0999 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGK1 | NM_001143676.3 | c.-368G>C | 5_prime_UTR_variant | 1/14 | ENST00000367858.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGK1 | ENST00000367858.10 | c.-368G>C | 5_prime_UTR_variant | 1/14 | 1 | NM_001143676.3 | |||
SGK1 | ENST00000461976.2 | c.-38G>C | 5_prime_UTR_variant | 1/6 | 4 | ||||
SGK1 | ENST00000533224.1 | c.-96G>C | 5_prime_UTR_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0736 AC: 11207AN: 152168Hom.: 488 Cov.: 32
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GnomAD4 exome AF: 0.0956 AC: 5218AN: 54572Hom.: 281 Cov.: 0 AF XY: 0.0961 AC XY: 2667AN XY: 27754
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GnomAD4 genome ? AF: 0.0736 AC: 11201AN: 152286Hom.: 490 Cov.: 32 AF XY: 0.0745 AC XY: 5548AN XY: 74458
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at