rs4896028

Positions:

• chr6-134218041-G-A
• chr6-134218041-G-C

Variant summary

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

The NM_001143676.3(SGK1):​c.286-10610C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,070 control chromosomes in the GnomAD database, including 31,279 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 0.61 (31279 hom., cov: 32)
• Consequence: SGK1 NM_001143676.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGK1	NM_001143676.3	c.286-10610C>T		intron_variant		ENST00000367858.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGK1	ENST00000367858.10	c.286-10610C>T		intron_variant		1	NM_001143676.3

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93411 AN: 151952 Hom.: 31276 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.614 AC: 93430 AN: 152070 Hom.: 31279 Cov.: 32 AF XY: 0.623 AC XY: 46353 AN XY: 74356

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.625

Alfa AF: 0.710 Hom.: 78317

Bravo AF: 0.583

Asia WGS AF: 0.713 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4896028; hg19: chr6-134539179;