rs1763510

chr6-134236069-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+25864A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,928 control chromosomes in the GnomAD database, including 21,660 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 0.48 (21660 hom., cov: 30)
• Consequence: SGK1 NM_001143676.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGK1	NM_001143676.3	c.285+25864A>G		intron_variant		ENST00000367858.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGK1	ENST00000367858.10	c.285+25864A>G		intron_variant		1	NM_001143676.3

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73589 AN: 151810 Hom.: 21660 Cov.: 30

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.484 AC: 73588 AN: 151928 Hom.: 21660 Cov.: 30 AF XY: 0.495 AC XY: 36714 AN XY: 74224

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.506

Alfa AF: 0.604 Hom.: 52736

Bravo AF: 0.448

Asia WGS AF: 0.643 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.6
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1763510; hg19: chr6-134557207;