17-4631613-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001140.5(ALOX15):c.1976G>T(p.Ser659Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000031 in 1,613,122 control chromosomes in the GnomAD database, with no homozygous occurrence. 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.1976G>T | p.Ser659Ile | missense_variant | Exon 14 of 14 | 1 | NM_001140.5 | ENSP00000293761.3 | ||
ALOX15 | ENST00000570836.6 | c.1976G>T | p.Ser659Ile | missense_variant | Exon 15 of 15 | 2 | ENSP00000458832.1 | |||
ALOX15 | ENST00000574640.1 | c.1859G>T | p.Ser620Ile | missense_variant | Exon 14 of 14 | 2 | ENSP00000460483.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251170Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135744
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460956Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726782
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1976G>T (p.S659I) alteration is located in exon 14 (coding exon 14) of the ALOX15 gene. This alteration results from a G to T substitution at nucleotide position 1976, causing the serine (S) at amino acid position 659 to be replaced by an isoleucine (I). 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