7-102467397-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152892.3(LRWD1):āc.491A>Gā(p.Lys164Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,613,642 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRWD1 | NM_152892.3 | c.491A>G | p.Lys164Arg | missense_variant | Exon 4 of 15 | ENST00000292616.10 | NP_690852.1 | |
LRWD1 | NM_001317721.2 | c.35A>G | p.Lys12Arg | missense_variant | Exon 4 of 15 | NP_001304650.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151966Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250328Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135534
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461676Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727136
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151966Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74228
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.491A>G (p.K164R) 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 491, causing the lysine (K) at amino acid position 164 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