8-132024687-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080399.3(OC90):c.1228C>T(p.Leu410Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,613,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OC90 | ENST00000254627.4 | c.1228C>T | p.Leu410Phe | missense_variant | Exon 14 of 14 | 2 | NM_001080399.3 | ENSP00000254627.3 | ||
ENSG00000258417 | ENST00000262283.5 | c.1864C>T | p.Leu622Phe | missense_variant | Exon 18 of 18 | 5 | ENSP00000262283.5 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000485 AC: 12AN: 247472Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134492
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461432Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727006
GnomAD4 genome AF: 0.000243 AC: 37AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1228C>T (p.L410F) alteration is located in exon 14 (coding exon 13) of the OC90 gene. This alteration results from a C to T substitution at nucleotide position 1228, causing the leucine (L) at amino acid position 410 to be replaced by a phenylalanine (F). 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