8-89921141-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001126111.3(OSGIN2):āc.590A>Cā(p.Lys197Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000723 in 1,603,468 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001126111.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OSGIN2 | NM_001126111.3 | c.590A>C | p.Lys197Thr | missense_variant | 5/6 | ENST00000451899.7 | NP_001119583.1 | |
OSGIN2 | NM_004337.2 | c.458A>C | p.Lys153Thr | missense_variant | 5/6 | NP_004328.1 | ||
OSGIN2 | XM_011517287.4 | c.458A>C | p.Lys153Thr | missense_variant | 5/6 | XP_011515589.1 | ||
OSGIN2 | XM_011517288.4 | c.59A>C | p.Lys20Thr | missense_variant | 2/3 | XP_011515590.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OSGIN2 | ENST00000451899.7 | c.590A>C | p.Lys197Thr | missense_variant | 5/6 | 1 | NM_001126111.3 | ENSP00000396445 | ||
OSGIN2 | ENST00000297438.6 | c.458A>C | p.Lys153Thr | missense_variant | 5/6 | 1 | ENSP00000297438 | P1 | ||
OSGIN2 | ENST00000647849.1 | c.458A>C | p.Lys153Thr | missense_variant | 5/6 | ENSP00000497119 | P1 | |||
OSGIN2 | ENST00000520659.1 | c.590A>C | p.Lys197Thr | missense_variant | 5/5 | 2 | ENSP00000431029 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247708Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133966
GnomAD4 exome AF: 0.0000772 AC: 112AN: 1451280Hom.: 0 Cov.: 27 AF XY: 0.0000637 AC XY: 46AN XY: 722510
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2024 | The c.590A>C (p.K197T) alteration is located in exon 5 (coding exon 5) of the OSGIN2 gene. This alteration results from a A to C substitution at nucleotide position 590, causing the lysine (K) at amino acid position 197 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