8-66822373-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001033578.3(SGK3):c.331C>A(p.Pro111Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,601,302 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001033578.3 missense, splice_region
Scores
Clinical Significance
Conservation
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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.331C>A | p.Pro111Thr | missense_variant, splice_region_variant | 6/17 | ENST00000521198.7 | |
C8orf44-SGK3 | NM_001204173.2 | c.331C>A | p.Pro111Thr | missense_variant, splice_region_variant | 8/19 | ||
SGK3 | NM_013257.5 | c.331C>A | p.Pro111Thr | missense_variant, splice_region_variant | 6/17 | ||
SGK3 | NM_170709.3 | c.331C>A | p.Pro111Thr | missense_variant, splice_region_variant | 6/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGK3 | ENST00000521198.7 | c.331C>A | p.Pro111Thr | missense_variant, splice_region_variant | 6/17 | 1 | NM_001033578.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 152002Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000369 AC: 9AN: 244024Hom.: 0 AF XY: 0.0000227 AC XY: 3AN XY: 131894
GnomAD4 exome AF: 0.0000104 AC: 15AN: 1449182Hom.: 0 Cov.: 30 AF XY: 0.00000833 AC XY: 6AN XY: 720352
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.331C>A (p.P111T) alteration is located in exon 6 (coding exon 5) of the SGK3 gene. This alteration results from a C to A substitution at nucleotide position 331, causing the proline (P) at amino acid position 111 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at