rs9493873

chr6-134255373-T-C

Variant summary

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

The NM_001143676.3(SGK1):c.285+6560A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 151,954 control chromosomes in the GnomAD database, including 222 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 0.041 (222 hom., cov: 31)
• Consequence: SGK1 NM_001143676.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

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=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGK1	NM_001143676.3	c.285+6560A>G		intron_variant		ENST00000367858.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGK1	ENST00000367858.10	c.285+6560A>G		intron_variant		1	NM_001143676.3
SGK1	ENST00000460769.1	c.127+6560A>G		intron_variant		3
SGK1	ENST00000461976.2	c.192+6560A>G		intron_variant		4
SGK1	ENST00000484353.1	n.85+6560A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0406 AC: 6161 AN: 151836 Hom.: 224 Cov.: 31

Gnomad AFR AF: 0.0576

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0798

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0849

Gnomad FIN AF: 0.0192

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0408

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

GnomAD4 genome AF: 0.0406 AC: 6166 AN: 151954 Hom.: 222 Cov.: 31 AF XY: 0.0418 AC XY: 3101 AN XY: 74274

Gnomad4 AFR AF: 0.0576

Gnomad4 AMR AF: 0.0798

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.0850

Gnomad4 FIN AF: 0.0192

Gnomad4 NFE AF: 0.0179

Gnomad4 OTH AF: 0.0399

Alfa AF: 0.0265 Hom.: 82

Bravo AF: 0.0470

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	11
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9493873; hg19: chr6-134576511;