7-102467382-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152892.3(LRWD1):āc.476A>Cā(p.Glu159Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,372 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRWD1 | NM_152892.3 | c.476A>C | p.Glu159Ala | missense_variant | Exon 4 of 15 | ENST00000292616.10 | NP_690852.1 | |
LRWD1 | NM_001317721.2 | c.20A>C | p.Glu7Ala | missense_variant | Exon 4 of 15 | NP_001304650.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151942Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461430Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726966
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151942Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74204
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.476A>C (p.E159A) alteration is located in exon 4 (coding exon 4) of the LRWD1 gene. This alteration results from a A to C substitution at nucleotide position 476, causing the glutamic acid (E) at amino acid position 159 to be replaced by an alanine (A). 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