chr8-66804396-A-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001033578.3(SGK3):āc.202A>Gā(p.Met68Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000685 in 1,459,070 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.0000069 ( 0 hom. )
Consequence
SGK3
NM_001033578.3 missense
NM_001033578.3 missense
Scores
3
14
Clinical Significance
Conservation
PhyloP100: 4.44
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.29267102).
BS2
High AC in GnomAdExome4 at 10 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGK3 | NM_001033578.3 | c.202A>G | p.Met68Val | missense_variant | 4/17 | ENST00000521198.7 | |
C8orf44-SGK3 | NM_001204173.2 | c.202A>G | p.Met68Val | missense_variant | 6/19 | ||
SGK3 | NM_013257.5 | c.202A>G | p.Met68Val | missense_variant | 4/17 | ||
SGK3 | NM_170709.3 | c.202A>G | p.Met68Val | missense_variant | 4/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGK3 | ENST00000521198.7 | c.202A>G | p.Met68Val | missense_variant | 4/17 | 1 | NM_001033578.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1459070Hom.: 0 Cov.: 30 AF XY: 0.00000965 AC XY: 7AN XY: 725728
GnomAD4 exome
AF:
AC:
10
AN:
1459070
Hom.:
Cov.:
30
AF XY:
AC XY:
7
AN XY:
725728
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2024 | The c.202A>G (p.M68V) alteration is located in exon 4 (coding exon 3) of the SGK3 gene. This alteration results from a A to G substitution at nucleotide position 202, causing the methionine (M) at amino acid position 68 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.;T;.;.;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N;.;N;.;N;.;N;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;D;T;T;T;T;T;D
Sift4G
Benign
T;T;T;T;T;T;T;T;T;D
Polyphen
B;B;B;.;B;.;B;.;B;.
Vest4
MutPred
Gain of catalytic residue at Q64 (P = 0.1037);Gain of catalytic residue at Q64 (P = 0.1037);Gain of catalytic residue at Q64 (P = 0.1037);.;Gain of catalytic residue at Q64 (P = 0.1037);Gain of catalytic residue at Q64 (P = 0.1037);Gain of catalytic residue at Q64 (P = 0.1037);Gain of catalytic residue at Q64 (P = 0.1037);Gain of catalytic residue at Q64 (P = 0.1037);.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at