rs9389154

Variant names:

• chr6-134293623-G-A
• rs9389154
• NM_001143676.3:c.69+23769C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-134293623-G-A
• chr6-134293623-G-C
• chr6-134293623-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.69+23769C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,092 control chromosomes in the GnomAD database, including 1,562 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 0.12 (1562 hom., cov: 32)
• Consequence: SGK1 NM_001143676.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898

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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGK1	NM_001143676.3	c.69+23769C>T		intron_variant	Intron 1 of 13	ENST00000367858.10	NP_001137148.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGK1	ENST00000367858.10	c.69+23769C>T		intron_variant	Intron 1 of 13	1	NM_001143676.3	ENSP00000356832.5
SGK1	ENST00000524929.1	c.69+23769C>T		intron_variant	Intron 1 of 1	1		ENSP00000435724.1
SGK1	ENST00000461976.2	c.-25+24192C>T		intron_variant	Intron 1 of 5	4		ENSP00000435577.1
SGK1	ENST00000533224.1	c.69+23769C>T		intron_variant	Intron 2 of 2	4		ENSP00000436470.1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17781 AN: 151974 Hom.: 1564 Cov.: 32

Gnomad AFR AF: 0.0684

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0639

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.117 AC: 17795 AN: 152092 Hom.: 1562 Cov.: 32 AF XY: 0.120 AC XY: 8947 AN XY: 74342

Gnomad4 AFR AF: 0.0684

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0639

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.109

Alfa AF: 0.113 Hom.: 1508

Bravo AF: 0.121

Asia WGS AF: 0.264 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	10
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9389154; hg19: chr6-134614761;