6-134199758-T-C

Variant names:

• chr6-134199758-T-C
• rs1743955
• NM_001143676.3:c.361+7598A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001143676.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGK1	NM_001143676.3	MANE Select	c.361+7598A>G		intron	N/A	NP_001137148.1	O00141-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGK1	ENST00000367858.10	TSL:1 MANE Select	c.361+7598A>G		intron	N/A	ENSP00000356832.5	O00141-2
	SGK1	ENST00000944482.1		c.145+7598A>G		intron	N/A	ENSP00000614541.1
	SGK1	ENST00000461976.2	TSL:4	c.268+7598A>G		intron	N/A	ENSP00000435577.1	E9PJN2

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

African (AFR) AF: 0.389 AC: 16104 AN: 41388

American (AMR) AF: 0.428 AC: 6513 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2050 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1016 AN: 5162

South Asian (SAS) AF: 0.488 AC: 2351 AN: 4818

European-Finnish (FIN) AF: 0.654 AC: 6845 AN: 10460

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41511 AN: 67902

Other (OTH) AF: 0.492 AC: 1039 AN: 2112

Alfa AF: 0.575 Hom.: 12429

Bravo AF: 0.488

Asia WGS AF: 0.331 AC: 1149 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.9
DANN	Benign	0.83
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1743955; hg19: chr6-134520896;