7-102467444-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_152892.3(LRWD1):c.538G>A(p.Gly180Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,638 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_152892.3 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 |
---|---|---|---|---|---|---|---|---|
LRWD1 | NM_152892.3 | c.538G>A | p.Gly180Arg | missense_variant | Exon 4 of 15 | ENST00000292616.10 | NP_690852.1 | |
LRWD1 | NM_001317721.2 | c.82G>A | p.Gly28Arg | missense_variant | Exon 4 of 15 | NP_001304650.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151942Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250636Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135638
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461696Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 727144
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151942Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74202
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.538G>A (p.G180R) alteration is located in exon 4 (coding exon 4) of the LRWD1 gene. This alteration results from a G to A substitution at nucleotide position 538, causing the glycine (G) at amino acid position 180 to be replaced by an arginine (R). 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