chr8-89924709-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001126111.3(OSGIN2):āc.827A>Gā(p.Lys276Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,614,132 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OSGIN2 | NM_001126111.3 | c.827A>G | p.Lys276Arg | missense_variant | 6/6 | ENST00000451899.7 | NP_001119583.1 | |
OSGIN2 | NM_004337.2 | c.695A>G | p.Lys232Arg | missense_variant | 6/6 | NP_004328.1 | ||
OSGIN2 | XM_011517287.4 | c.695A>G | p.Lys232Arg | missense_variant | 6/6 | XP_011515589.1 | ||
OSGIN2 | XM_011517288.4 | c.296A>G | p.Lys99Arg | missense_variant | 3/3 | XP_011515590.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OSGIN2 | ENST00000451899.7 | c.827A>G | p.Lys276Arg | missense_variant | 6/6 | 1 | NM_001126111.3 | ENSP00000396445 | ||
OSGIN2 | ENST00000297438.6 | c.695A>G | p.Lys232Arg | missense_variant | 6/6 | 1 | ENSP00000297438 | P1 | ||
OSGIN2 | ENST00000647849.1 | c.695A>G | p.Lys232Arg | missense_variant | 6/6 | ENSP00000497119 | P1 | |||
NBN | ENST00000697292.1 | c.*671T>C | 3_prime_UTR_variant | 17/17 | ENSP00000513229 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000678 AC: 17AN: 250786Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135504
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461766Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727194
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152366Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74522
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.827A>G (p.K276R) alteration is located in exon 6 (coding exon 6) of the OSGIN2 gene. This alteration results from a A to G substitution at nucleotide position 827, causing the lysine (K) at amino acid position 276 to be replaced by an arginine (R). 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