chr8-23309795-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002318.3(LOXL2):c.1753G>A(p.Ala585Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00002 in 1,603,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002318.3 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 |
---|---|---|---|---|---|---|---|
LOXL2 | NM_002318.3 | c.1753G>A | p.Ala585Thr | missense_variant | 10/14 | ENST00000389131.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXL2 | ENST00000389131.8 | c.1753G>A | p.Ala585Thr | missense_variant | 10/14 | 1 | NM_002318.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000331 AC: 8AN: 241986Hom.: 0 AF XY: 0.0000305 AC XY: 4AN XY: 131050
GnomAD4 exome AF: 0.0000152 AC: 22AN: 1451312Hom.: 0 Cov.: 30 AF XY: 0.0000180 AC XY: 13AN XY: 721596
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 07, 2022 | The c.1753G>A (p.A585T) alteration is located in exon 10 (coding exon 9) of the LOXL2 gene. This alteration results from a G to A substitution at nucleotide position 1753, causing the alanine (A) at amino acid position 585 to be replaced by a threonine (T). 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