dbSNP rs3813344: SGK1:c.-368G>C (chr6-134317828-C-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.-368G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0794 in 206,858 control chromosomes in the GnomAD database, including 771 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 0.074 ( 490 hom., cov: 32)

Exomes 𝑓: 0.096 ( 281 hom. )

Consequence

SGK1
NM_001143676.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.284

Publications

6 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0999 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGK1	NM_001143676.3	MANE Select	c.-368G>C		5_prime_UTR	Exon 1 of 14	NP_001137148.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SGK1	ENST00000367858.10	TSL:1 MANE Select	c.-368G>C	5_prime_UTR	Exon 1 of 14	ENSP00000356832.5
SGK1	ENST00000461976.2	TSL:4	c.-38G>C	5_prime_UTR	Exon 1 of 6	ENSP00000435577.1
SGK1	ENST00000533224.1	TSL:4	c.-96G>C	5_prime_UTR	Exon 1 of 3	ENSP00000436470.1

Frequencies

GnomAD3 genomes

AF:

0.0736

AC:

11207

AN:

152168

Hom.:

488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0217

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.0652

Gnomad ASJ

AF:

0.0995

Gnomad EAS

AF:

0.0688

Gnomad SAS

AF:

0.0845

Gnomad FIN

AF:

0.0956

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.0789

GnomAD4 exome

AF:

0.0956

AC:

5218

AN:

54572

Hom.:

281

Cov.:

AF XY:

0.0961

AC XY:

2667

AN XY:

27754

show subpopulations

African (AFR)

AF:

0.0252

AC:

AN:

1984

American (AMR)

AF:

0.0827

AC:

165

AN:

1996

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

221

AN:

1934

East Asian (EAS)

AF:

0.0789

AC:

293

AN:

3712

South Asian (SAS)

AF:

0.0807

AC:

237

AN:

2936

European-Finnish (FIN)

AF:

0.102

AC:

275

AN:

2694

Middle Eastern (MID)

AF:

0.0826

AC:

AN:

242

European-Non Finnish (NFE)

AF:

0.102

AC:

3632

AN:

35570

Other (OTH)

AF:

0.0928

AC:

325

AN:

3504

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

237

474

712

949

1186

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

130

<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:

0.0736

AC:

11201

AN:

152286

Hom.:

490

Cov.:

AF XY:

0.0745

AC XY:

5548

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.0218

AC:

905

AN:

41576

American (AMR)

AF:

0.0652

AC:

997

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0995

AC:

345

AN:

3468

East Asian (EAS)

AF:

0.0682

AC:

352

AN:

5164

South Asian (SAS)

AF:

0.0844

AC:

407

AN:

4824

European-Finnish (FIN)

AF:

0.0956

AC:

1015

AN:

10618

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6933

AN:

68018

Other (OTH)

AF:

0.0776

AC:

164

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

535

1070

1606

2141

2676

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.0788

Hom.:

Bravo

AF:

0.0694

Asia WGS

AF:

0.0630

AC:

219

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

9.7

(source)

DANN

Benign

0.76

PhyloP100

0.28

PromoterAI

-0.012

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over