chr6-134281316-T-C

Position:

• chr6-134281316-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.70-19168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,948 control chromosomes in the GnomAD database, including 15,003 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 0.44 (15003 hom., cov: 31)
• Consequence: SGK1 NM_001143676.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SGK1	NM_001143676.3	c.70-19168A>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.70-19168A>G		intron_variant		1	NM_001143676.3	ENSP00000356832.5
SGK1	ENST00000524929.1	c.70-19168A>G		intron_variant		1		ENSP00000435724.1
SGK1	ENST00000461976.2	c.-24-19168A>G		intron_variant		4		ENSP00000435577.1
SGK1	ENST00000533224.1	c.70-19168A>G		intron_variant		4		ENSP00000436470.1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66095 AN: 151830 Hom.: 14996 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.435 AC: 66140 AN: 151948 Hom.: 15003 Cov.: 31 AF XY: 0.440 AC XY: 32670 AN XY: 74252

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.427

Alfa AF: 0.425 Hom.: 28732

Bravo AF: 0.439

Asia WGS AF: 0.524 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9376026; hg19: chr6-134602454;