7-102467403-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152892.3(LRWD1):āc.497A>Gā(p.Gln166Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000706 in 1,613,722 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_152892.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRWD1 | NM_152892.3 | c.497A>G | p.Gln166Arg | missense_variant | Exon 4 of 15 | ENST00000292616.10 | NP_690852.1 | |
LRWD1 | NM_001317721.2 | c.41A>G | p.Gln14Arg | missense_variant | Exon 4 of 15 | NP_001304650.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 151998Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000152 AC: 38AN: 250474Hom.: 0 AF XY: 0.000170 AC XY: 23AN XY: 135604
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461724Hom.: 0 Cov.: 32 AF XY: 0.0000729 AC XY: 53AN XY: 727150
GnomAD4 genome AF: 0.000125 AC: 19AN: 151998Hom.: 0 Cov.: 31 AF XY: 0.0000943 AC XY: 7AN XY: 74226
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.497A>G (p.Q166R) alteration is located in exon 4 (coding exon 4) of the LRWD1 gene. This alteration results from a A to G substitution at nucleotide position 497, causing the glutamine (Q) at amino acid position 166 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