2-111092905-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001142807.4(ACOXL):c.1481G>A(p.Arg494Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,722 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R494L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001142807.4 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 | UniProt |
---|---|---|---|---|---|---|---|
ACOXL | NM_001142807.4 | c.1481G>A | p.Arg494Gln | missense_variant | 17/18 | ENST00000439055.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACOXL | ENST00000439055.6 | c.1481G>A | p.Arg494Gln | missense_variant | 17/18 | 2 | NM_001142807.4 | ||
MIR4435-2HG | ENST00000645030.2 | n.453-55983C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151920Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251356Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135850
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461802Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 727204
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151920Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74192
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.1481G>A (p.R494Q) alteration is located in exon 17 (coding exon 16) of the ACOXL gene. This alteration results from a G to A substitution at nucleotide position 1481, causing the arginine (R) at amino acid position 494 to be replaced by a glutamine (Q). 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