14-22766746-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000612549.6(OXA1L):āc.45G>Cā(p.Leu15Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,614,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000612549.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OXA1L | NM_005015.5 | c.45G>C | p.Leu15Phe | missense_variant | 1/10 | ENST00000612549.6 | NP_005006.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OXA1L | ENST00000612549.6 | c.45G>C | p.Leu15Phe | missense_variant | 1/10 | 1 | NM_005015.5 | ENSP00000483491 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152260Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249940Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135460
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461866Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727236
GnomAD4 genome AF: 0.0000984 AC: 15AN: 152378Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74522
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2022 | The c.225G>C (p.L75F) alteration is located in exon 1 (coding exon 1) of the OXA1L gene. This alteration results from a G to C substitution at nucleotide position 225, causing the leucine (L) at amino acid position 75 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