chr8-23309713-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.1835G>A(p.Arg612Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000306 in 1,569,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R612W) has been classified 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.1835G>A | p.Arg612Gln | missense_variant | 10/14 | ENST00000389131.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXL2 | ENST00000389131.8 | c.1835G>A | p.Arg612Gln | missense_variant | 10/14 | 1 | NM_002318.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000564 AC: 12AN: 212780Hom.: 0 AF XY: 0.0000690 AC XY: 8AN XY: 115980
GnomAD4 exome AF: 0.0000261 AC: 37AN: 1417112Hom.: 0 Cov.: 30 AF XY: 0.0000299 AC XY: 21AN XY: 701838
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.1835G>A (p.R612Q) 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 1835, causing the arginine (R) at amino acid position 612 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