rs1763500

Positions:

• chr6-134223595-G-A
• chr6-134223595-G-C
• chr6-134223595-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001143676.3(SGK1):​c.286-16164C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 152,238 control chromosomes in the GnomAD database, including 62,190 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 0.90 (62190 hom., cov: 32)
• Consequence: SGK1 NM_001143676.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610

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]

SGK1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SGK1	NM_001143676.3	c.286-16164C>T		intron_variant		ENST00000367858.10	NP_001137148.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGK1	ENST00000367858.10	c.286-16164C>T		intron_variant		1	NM_001143676.3	ENSP00000356832.5

Frequencies

GnomAD3 genomes AF: 0.901 AC: 136990 AN: 152120 Hom.: 62151 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.901

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.900 AC: 137086 AN: 152238 Hom.: 62190 Cov.: 32 AF XY: 0.905 AC XY: 67390 AN XY: 74424

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.984

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.944

Gnomad4 OTH AF: 0.902

Alfa AF: 0.934 Hom.: 90042

Bravo AF: 0.890

Asia WGS AF: 0.980 AC: 3405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1763500; hg19: chr6-134544733;