dbSNP rs1743966: SGK1:c.835-35T>C (chr6-134172809-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001143676.3(SGK1):c.835-35T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 1,476,506 control chromosomes in the GnomAD database, including 34,906 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 0.24 ( 4546 hom., cov: 32)

Exomes 𝑓: 0.21 ( 30360 hom. )

Consequence

SGK1
NM_001143676.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.94

Publications

27 publications found

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGK1	NM_001143676.3 link	c.835-35T>C		intron_variant	Intron 8 of 13	ENST00000367858.10	NP_001137148.1	O00141-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGK1	ENST00000367858.10 link	c.835-35T>C		intron_variant	Intron 8 of 13	1	NM_001143676.3	ENSP00000356832.5		O00141-2

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36371

AN:

152008

Hom.:

4533

Cov.:

show subpopulations

Gnomad AFR

AF:

0.297

Gnomad AMI

AF:

0.100

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.289

Gnomad EAS

AF:

0.240

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.234

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.208

Gnomad OTH

AF:

0.248

GnomAD2 exomes

AF:

0.221

AC:

54321

AN:

245674

AF XY:

0.213

show subpopulations

Gnomad AFR exome

AF:

0.299

Gnomad AMR exome

AF:

0.276

Gnomad ASJ exome

AF:

0.288

Gnomad EAS exome

AF:

0.249

Gnomad FIN exome

AF:

0.236

Gnomad NFE exome

AF:

0.206

Gnomad OTH exome

AF:

0.226

GnomAD4 exome

AF:

0.211

AC:

279262

AN:

1324380

Hom.:

30360

Cov.:

AF XY:

0.208

AC XY:

138428

AN XY:

666460

show subpopulations

African (AFR)

AF:

0.299

AC:

9184

AN:

30676

American (AMR)

AF:

0.274

AC:

12025

AN:

43916

Ashkenazi Jewish (ASJ)

AF:

0.285

AC:

7191

AN:

25242

East Asian (EAS)

AF:

0.226

AC:

8809

AN:

38988

South Asian (SAS)

AF:

0.129

AC:

10701

AN:

83226

European-Finnish (FIN)

AF:

0.230

AC:

12258

AN:

53276

Middle Eastern (MID)

AF:

0.208

AC:

1151

AN:

5528

European-Non Finnish (NFE)

AF:

0.208

AC:

205640

AN:

987714

Other (OTH)

AF:

0.220

AC:

12303

AN:

55814

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

11228

22457

33685

44914

56142

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6894

13788

20682

27576

34470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.239

AC:

36418

AN:

152126

Hom.:

4546

Cov.:

AF XY:

0.237

AC XY:

17655

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.297

AC:

12344

AN:

41502

American (AMR)

AF:

0.254

AC:

3879

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.289

AC:

1004

AN:

3472

East Asian (EAS)

AF:

0.239

AC:

1239

AN:

5176

South Asian (SAS)

AF:

0.128

AC:

617

AN:

4828

European-Finnish (FIN)

AF:

0.234

AC:

2480

AN:

10582

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.208

AC:

14171

AN:

67978

Other (OTH)

AF:

0.245

AC:

517

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1387

2774

4160

5547

6934

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

374

748

1122

1496

1870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.221

Hom.:

10014

Bravo

AF:

0.247

Asia WGS

AF:

0.199

AC:

694

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

9.7

(source)

DANN

Benign

0.62

PhyloP100

1.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over