rs1763500

Variant names:

• chr6-134223595-G-A
• rs1763500
• NM_001143676.3:c.286-16164C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-134223595-G-A
• chr6-134223595-G-C
• chr6-134223595-G-T

Variant summary

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

The NM_001143676.3(SGK1):​c.286-16164C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 152,238 control chromosomes in the GnomAD database, including 62,190 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 0.90 (62190 hom., cov: 32)
• Consequence: SGK1 NM_001143676.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610
• Publications: 11 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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.286-16164C>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.286-16164C>T		intron	N/A	ENSP00000356832.5
	SGK1	ENST00000461976.2	TSL:4	c.193-16164C>T		intron	N/A	ENSP00000435577.1
	SGK1	ENST00000460769.1	TSL:3	c.127-8502C>T		intron	N/A	ENSP00000431705.1

Frequencies

GnomAD3 genomes AF: 0.901 AC: 136990 AN: 152120 Hom.: 62151 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.900 AC: 137086 AN: 152238 Hom.: 62190 Cov.: 32 AF XY: 0.905 AC XY: 67390 AN XY: 74424

African (AFR) AF: 0.772 AC: 32032 AN: 41502

American (AMR) AF: 0.928 AC: 14202 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3267 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5169 AN: 5174

South Asian (SAS) AF: 0.984 AC: 4753 AN: 4832

European-Finnish (FIN) AF: 0.983 AC: 10440 AN: 10618

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.944 AC: 64188 AN: 68028

Other (OTH) AF: 0.902 AC: 1901 AN: 2108

Alfa AF: 0.920 Hom.: 124950

Bravo AF: 0.890

Asia WGS AF: 0.980 AC: 3405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.63
PhyloP100		-0.61
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: rs1763500; hg19: chr6-134544733;