6-134199758-T-C

Position:

• chr6-134199758-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.361+7598A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,748 control chromosomes in the GnomAD database, including 21,346 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 0.52 (21346 hom., cov: 31)
• Consequence: SGK1 NM_001143676.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

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]

SGK1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SGK1	NM_001143676.3	c.361+7598A>G		intron_variant		ENST00000367858.10	NP_001137148.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGK1	ENST00000367858.10	c.361+7598A>G		intron_variant		1	NM_001143676.3	ENSP00000356832.5

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78132 AN: 151632 Hom.: 21333 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.515 AC: 78167 AN: 151748 Hom.: 21346 Cov.: 31 AF XY: 0.513 AC XY: 38091 AN XY: 74182

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.492

Alfa AF: 0.576 Hom.: 11019

Bravo AF: 0.488

Asia WGS AF: 0.331 AC: 1149 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.9
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1743955; hg19: chr6-134520896;