17-4632863-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001140.5(ALOX15):c.1538G>A(p.Arg513Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 18/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001140.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALOX15 | ENST00000293761.8 | c.1538G>A | p.Arg513Gln | missense_variant, splice_region_variant | Exon 11 of 14 | 1 | NM_001140.5 | ENSP00000293761.3 | ||
ALOX15 | ENST00000570836.6 | c.1538G>A | p.Arg513Gln | missense_variant, splice_region_variant | Exon 12 of 15 | 2 | ENSP00000458832.1 | |||
ALOX15 | ENST00000574640.1 | c.1421G>A | p.Arg474Gln | missense_variant, splice_region_variant | Exon 11 of 14 | 2 | ENSP00000460483.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251224Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135800
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461842Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727222
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1538G>A (p.R513Q) alteration is located in exon 11 (coding exon 11) of the ALOX15 gene. This alteration results from a G to A substitution at nucleotide position 1538, causing the arginine (R) at amino acid position 513 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