chr8-66843356-T-A

Position:

• chr8-66843356-T-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001033578.3(SGK3):​c.979-96T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00473 in 1,243,870 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency:
  • Genomes: 𝑓 0.0033 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0049 (24 hom.)
• Consequence: SGK3 NM_001033578.3 intron
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: -0.0520

Genes affected

SGK3 (HGNC:10812): (serum/glucocorticoid regulated kinase family member 3) This gene is a member of the Ser/Thr protein kinase family and encodes a phosphoprotein with a PX (phox homology) domain. The protein phosphorylates several target proteins and has a role in neutral amino acid transport and activation of potassium and chloride channels. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

C8orf44-SGK3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BS2: High AC in GnomAd4 at 505 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGK3	NM_001033578.3	c.979-96T>A		intron_variant		ENST00000521198.7
C8orf44-SGK3	NM_001204173.2	c.979-96T>A		intron_variant
SGK3	NM_013257.5	c.979-96T>A		intron_variant
SGK3	NM_170709.3	c.978+2246T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGK3	ENST00000521198.7	c.979-96T>A		intron_variant		1	NM_001033578.3	P1

Frequencies

GnomAD3 genomes AF: 0.00332 AC: 506 AN: 152216 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00301

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00514

Gnomad OTH AF: 0.00239

GnomAD4 exome AF: 0.00493 AC: 5377 AN: 1091536 Hom.: 24 AF XY: 0.00482 AC XY: 2658 AN XY: 551384

Gnomad4 AFR exome AF: 0.000663

Gnomad4 AMR exome AF: 0.00265

Gnomad4 ASJ exome AF: 0.0162

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00136

Gnomad4 FIN exome AF: 0.000572

Gnomad4 NFE exome AF: 0.00556

Gnomad4 OTH exome AF: 0.00458

GnomAD4 genome AF: 0.00332 AC: 505 AN: 152334 Hom.: 3 Cov.: 32 AF XY: 0.00287 AC XY: 214 AN XY: 74504

Gnomad4 AFR AF: 0.00115

Gnomad4 AMR AF: 0.00301

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00514

Gnomad4 OTH AF: 0.00236

Alfa AF: 0.00408 Hom.: 1

Bravo AF: 0.00357

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, no assertion criteria provided

literature only

OMIM

Feb 17, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.3
DANN	Benign	0.81

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

LitVar

Other links and lift over

dbSNP: rs191330440; hg19: chr8-67755591;