8-132024666-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080399.3(OC90):c.1249G>A(p.Gly417Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,170 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001080399.3 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 |
---|---|---|---|---|---|---|---|---|
OC90 | NM_001080399.3 | c.1249G>A | p.Gly417Arg | missense_variant | 14/14 | ENST00000254627.4 | NP_001073868.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OC90 | ENST00000254627.4 | c.1249G>A | p.Gly417Arg | missense_variant | 14/14 | 2 | NM_001080399.3 | ENSP00000254627.3 | ||
ENSG00000258417 | ENST00000262283.5 | c.1885G>A | p.Gly629Arg | missense_variant | 18/18 | 5 | ENSP00000262283.5 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000325 AC: 8AN: 246164Hom.: 0 AF XY: 0.0000522 AC XY: 7AN XY: 133990
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460996Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726756
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 13, 2024 | The c.1249G>A (p.G417R) alteration is located in exon 14 (coding exon 13) of the OC90 gene. This alteration results from a G to A substitution at nucleotide position 1249, causing the glycine (G) at amino acid position 417 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