8-89924906-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001126111.3(OSGIN2):c.1024C>T(p.Arg342Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,614,128 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 (★).
Frequency
Consequence
NM_001126111.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OSGIN2 | NM_001126111.3 | c.1024C>T | p.Arg342Cys | missense_variant | 6/6 | ENST00000451899.7 | NP_001119583.1 | |
OSGIN2 | NM_004337.2 | c.892C>T | p.Arg298Cys | missense_variant | 6/6 | NP_004328.1 | ||
OSGIN2 | XM_011517287.4 | c.892C>T | p.Arg298Cys | missense_variant | 6/6 | XP_011515589.1 | ||
OSGIN2 | XM_011517288.4 | c.493C>T | p.Arg165Cys | missense_variant | 3/3 | XP_011515590.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OSGIN2 | ENST00000451899.7 | c.1024C>T | p.Arg342Cys | missense_variant | 6/6 | 1 | NM_001126111.3 | ENSP00000396445 | ||
OSGIN2 | ENST00000297438.6 | c.892C>T | p.Arg298Cys | missense_variant | 6/6 | 1 | ENSP00000297438 | P1 | ||
OSGIN2 | ENST00000647849.1 | c.892C>T | p.Arg298Cys | missense_variant | 6/6 | ENSP00000497119 | P1 | |||
NBN | ENST00000697292.1 | c.*474G>A | 3_prime_UTR_variant | 17/17 | ENSP00000513229 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250894Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135554
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461860Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727228
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 13, 2023 | The c.1024C>T (p.R342C) alteration is located in exon 6 (coding exon 6) of the OSGIN2 gene. This alteration results from a C to T substitution at nucleotide position 1024, causing the arginine (R) at amino acid position 342 to be replaced by a cysteine (C). 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