16-83965328-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_182981.3(OSGIN1):c.755C>T(p.Pro252Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000952 in 1,576,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182981.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OSGIN1 | ENST00000393306.6 | c.755C>T | p.Pro252Leu | missense_variant | Exon 6 of 6 | 1 | NM_182981.3 | ENSP00000376983.1 | ||
OSGIN1 | ENST00000361711.7 | c.755C>T | p.Pro252Leu | missense_variant | Exon 6 of 6 | 2 | ENSP00000355374.3 | |||
OSGIN1 | ENST00000343939.6 | n.1387C>T | non_coding_transcript_exon_variant | Exon 7 of 7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000139 AC: 3AN: 216538Hom.: 0 AF XY: 0.0000256 AC XY: 3AN XY: 117416
GnomAD4 exome AF: 0.00000492 AC: 7AN: 1423862Hom.: 0 Cov.: 34 AF XY: 0.00000568 AC XY: 4AN XY: 703970
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.755C>T (p.P252L) alteration is located in exon 6 (coding exon 5) of the OSGIN1 gene. This alteration results from a C to T substitution at nucleotide position 755, causing the proline (P) at amino acid position 252 to be replaced by a leucine (L). 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