5-97096850-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_153234.5(LIX1):c.521G>A(p.Gly174Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000269 in 1,614,030 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_153234.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIX1 | NM_153234.5 | c.521G>A | p.Gly174Glu | missense_variant | Exon 5 of 6 | ENST00000274382.9 | NP_694966.3 | |
LIX1-AS1 | NR_187470.1 | n.345-2087C>T | intron_variant | Intron 4 of 7 | ||||
LIX1-AS1 | NR_187471.1 | n.226-4909C>T | intron_variant | Intron 2 of 3 | ||||
LIX1-AS1 | NR_187472.1 | n.115-2087C>T | intron_variant | Intron 1 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251438Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135896
GnomAD4 exome AF: 0.000274 AC: 401AN: 1461734Hom.: 0 Cov.: 30 AF XY: 0.000254 AC XY: 185AN XY: 727180
GnomAD4 genome AF: 0.000217 AC: 33AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.521G>A (p.G174E) alteration is located in exon 5 (coding exon 5) of the LIX1 gene. This alteration results from a G to A substitution at nucleotide position 521, causing the glycine (G) at amino acid position 174 to be replaced by a glutamic acid (E). 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