rs1763509

Positions:

• chr6-134233200-G-A
• chr6-134233200-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.286-25769C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 152,040 control chromosomes in the GnomAD database, including 29,856 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 0.59 (29856 hom., cov: 32)
• Consequence: SGK1 NM_001143676.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SGK1	NM_001143676.3	c.286-25769C>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.286-25769C>T		intron_variant		1	NM_001143676.3	ENSP00000356832

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90307 AN: 151922 Hom.: 29855 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.594 AC: 90328 AN: 152040 Hom.: 29856 Cov.: 32 AF XY: 0.600 AC XY: 44630 AN XY: 74330

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.598

Alfa AF: 0.698 Hom.: 14684

Bravo AF: 0.559

Asia WGS AF: 0.713 AC: 2476 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.17
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1763509; hg19: chr6-134554338;