16-83965096-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_182981.3(OSGIN1):āc.523A>Gā(p.Ile175Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000269 in 1,601,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_182981.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OSGIN1 | ENST00000393306.6 | c.523A>G | p.Ile175Val | missense_variant | Exon 6 of 6 | 1 | NM_182981.3 | ENSP00000376983.1 | ||
OSGIN1 | ENST00000361711.7 | c.523A>G | p.Ile175Val | missense_variant | Exon 6 of 6 | 2 | ENSP00000355374.3 | |||
OSGIN1 | ENST00000343939.6 | n.1155A>G | non_coding_transcript_exon_variant | Exon 7 of 7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000159 AC: 24AN: 151408Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248664Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134706
GnomAD4 exome AF: 0.0000131 AC: 19AN: 1449634Hom.: 0 Cov.: 34 AF XY: 0.00000694 AC XY: 5AN XY: 720286
GnomAD4 genome AF: 0.000159 AC: 24AN: 151408Hom.: 0 Cov.: 33 AF XY: 0.000122 AC XY: 9AN XY: 73994
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.523A>G (p.I175V) alteration is located in exon 6 (coding exon 5) of the OSGIN1 gene. This alteration results from a A to G substitution at nucleotide position 523, causing the isoleucine (I) at amino acid position 175 to be replaced by a valine (V). 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