15-73927241-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005576.4(LOXL1):c.458G>T(p.Gly153Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000125 in 1,597,618 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G153D) has been classified as Benign.
Frequency
Consequence
NM_005576.4 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 |
---|---|---|---|---|---|---|---|
LOXL1 | NM_005576.4 | c.458G>T | p.Gly153Val | missense_variant | 1/7 | ENST00000261921.8 | |
LOXL1-AS1 | NR_040069.1 | n.184+824C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXL1 | ENST00000261921.8 | c.458G>T | p.Gly153Val | missense_variant | 1/7 | 1 | NM_005576.4 | P1 | |
LOXL1-AS1 | ENST00000685373.1 | n.198+536C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151998Hom.: 0 Cov.: 33
GnomAD4 exome AF: 6.92e-7 AC: 1AN: 1445620Hom.: 0 Cov.: 40 AF XY: 0.00 AC XY: 0AN XY: 719622
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151998Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74260
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at