5-97107472-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_153234.5(LIX1):c.275G>A(p.Arg92Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,613,758 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R92W) has been classified as Uncertain significance.
Frequency
Consequence
NM_153234.5 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 |
---|---|---|---|---|---|---|---|---|---|---|
LIX1 | ENST00000274382.9 | c.275G>A | p.Arg92Gln | missense_variant | Exon 3 of 6 | 1 | NM_153234.5 | ENSP00000274382.4 | ||
LIX1-AS1 | ENST00000504578.2 | n.573+4378C>T | intron_variant | Intron 3 of 6 | 5 | |||||
LIX1 | ENST00000512378.1 | c.*12G>A | downstream_gene_variant | 5 | ENSP00000427469.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251390Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135852
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461612Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727108
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.275G>A (p.R92Q) alteration is located in exon 3 (coding exon 3) of the LIX1 gene. This alteration results from a G to A substitution at nucleotide position 275, causing the arginine (R) at amino acid position 92 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