NM_001143676.3:c.285+25864A>G

Variant names:

• chr6-134236069-T-C
• rs1763510
• NM_001143676.3:c.285+25864A>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.285+25864A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,928 control chromosomes in the GnomAD database, including 21,660 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 0.48 (21660 hom., cov: 30)
• Consequence: SGK1 NM_001143676.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGK1	NM_001143676.3	c.285+25864A>G		intron_variant	Intron 2 of 13	ENST00000367858.10	NP_001137148.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGK1	ENST00000367858.10	c.285+25864A>G		intron_variant	Intron 2 of 13	1	NM_001143676.3	ENSP00000356832.5

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73589 AN: 151810 Hom.: 21660 Cov.: 30

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.484 AC: 73588 AN: 151928 Hom.: 21660 Cov.: 30 AF XY: 0.495 AC XY: 36714 AN XY: 74224

African (AFR) AF: 0.135 AC: 5594 AN: 41474

American (AMR) AF: 0.473 AC: 7214 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2200 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3424 AN: 5130

South Asian (SAS) AF: 0.771 AC: 3709 AN: 4808

European-Finnish (FIN) AF: 0.686 AC: 7218 AN: 10524

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42440 AN: 67948

Other (OTH) AF: 0.506 AC: 1066 AN: 2108

Alfa AF: 0.581 Hom.: 113109

Bravo AF: 0.448

Asia WGS AF: 0.643 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.75
PhyloP100		0.013
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: rs1763510; hg19: chr6-134557207;