rs4896028

Variant names:

• chr6-134218041-G-A
• rs4896028
• NM_001143676.3:c.286-10610C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-134218041-G-A
• chr6-134218041-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001143676.3(SGK1):​c.286-10610C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,070 control chromosomes in the GnomAD database, including 31,279 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 0.61 (31279 hom., cov: 32)
• Consequence: SGK1 NM_001143676.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 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.286-10610C>T		intron	N/A	NP_001137148.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGK1	ENST00000367858.10	TSL:1 MANE Select	c.286-10610C>T		intron	N/A	ENSP00000356832.5
	SGK1	ENST00000461976.2	TSL:4	c.193-10610C>T		intron	N/A	ENSP00000435577.1
	SGK1	ENST00000460769.1	TSL:3	c.127-2948C>T		intron	N/A	ENSP00000431705.1

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93411 AN: 151952 Hom.: 31276 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.614 AC: 93430 AN: 152070 Hom.: 31279 Cov.: 32 AF XY: 0.623 AC XY: 46353 AN XY: 74356

African (AFR) AF: 0.333 AC: 13809 AN: 41436

American (AMR) AF: 0.589 AC: 8992 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2553 AN: 3472

East Asian (EAS) AF: 0.710 AC: 3686 AN: 5190

South Asian (SAS) AF: 0.835 AC: 4032 AN: 4826

European-Finnish (FIN) AF: 0.795 AC: 8404 AN: 10572

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49747 AN: 67990

Other (OTH) AF: 0.625 AC: 1319 AN: 2112

Alfa AF: 0.695 Hom.: 160634

Bravo AF: 0.583

Asia WGS AF: 0.713 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.12
PhyloP100		-1.2
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: rs4896028; hg19: chr6-134539179;