17-4632014-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001140.5(ALOX15):c.1684C>T(p.Arg562Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,613,528 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001140.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALOX15 | ENST00000293761.8 | c.1684C>T | p.Arg562Trp | missense_variant | Exon 13 of 14 | 1 | NM_001140.5 | ENSP00000293761.3 | ||
ALOX15 | ENST00000570836.6 | c.1684C>T | p.Arg562Trp | missense_variant | Exon 14 of 15 | 2 | ENSP00000458832.1 | |||
ALOX15 | ENST00000574640.1 | c.1567C>T | p.Arg523Trp | missense_variant | Exon 13 of 14 | 2 | ENSP00000460483.1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152212Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.0000799 AC: 20AN: 250426Hom.: 0 AF XY: 0.0000886 AC XY: 12AN XY: 135370
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461198Hom.: 0 Cov.: 33 AF XY: 0.0000660 AC XY: 48AN XY: 726858
GnomAD4 genome AF: 0.000112 AC: 17AN: 152330Hom.: 1 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1684C>T (p.R562W) alteration is located in exon 13 (coding exon 13) of the ALOX15 gene. This alteration results from a C to T substitution at nucleotide position 1684, causing the arginine (R) at amino acid position 562 to be replaced by a tryptophan (W). 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