rs193920898
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001033578.3(SGK3):āc.782A>Gā(p.His261Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,784 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001033578.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGK3 | NM_001033578.3 | c.782A>G | p.His261Arg | missense_variant | 11/17 | ENST00000521198.7 | |
C8orf44-SGK3 | NM_001204173.2 | c.782A>G | p.His261Arg | missense_variant | 13/19 | ||
SGK3 | NM_013257.5 | c.782A>G | p.His261Arg | missense_variant | 11/17 | ||
SGK3 | NM_170709.3 | c.782A>G | p.His261Arg | missense_variant | 11/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGK3 | ENST00000521198.7 | c.782A>G | p.His261Arg | missense_variant | 11/17 | 1 | NM_001033578.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251424Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135882
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461784Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727180
GnomAD4 genome ? Cov.: 30
ClinVar
Submissions by phenotype
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Science for Life laboratory, Karolinska Institutet | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at