rs1763527

chr6-134178716-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.362-4130A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,126 control chromosomes in the GnomAD database, including 14,404 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 0.42 (14404 hom., cov: 33)
• Consequence: SGK1 NM_001143676.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGK1	NM_001143676.3	c.362-4130A>G		intron_variant		ENST00000367858.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGK1	ENST00000367858.10	c.362-4130A>G		intron_variant		1	NM_001143676.3
SGK1	ENST00000461976.2	c.269-4130A>G		intron_variant		4
SGK1	ENST00000524387.5	n.145-4130A>G		intron_variant, non_coding_transcript_variant		4
SGK1	ENST00000531575.5	n.162-4130A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64319 AN: 152008 Hom.: 14399 Cov.: 33

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.423 AC: 64340 AN: 152126 Hom.: 14404 Cov.: 33 AF XY: 0.419 AC XY: 31154 AN XY: 74362

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.399

Alfa AF: 0.479 Hom.: 38509

Bravo AF: 0.408

Asia WGS AF: 0.261 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.5
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1763527; hg19: chr6-134499854;