7-102465129-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152892.3(LRWD1):c.49A>T(p.Ser17Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000046 in 1,520,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRWD1 | NM_152892.3 | c.49A>T | p.Ser17Cys | missense_variant | Exon 1 of 15 | ENST00000292616.10 | NP_690852.1 | |
LRWD1 | NM_001317721.2 | c.-426A>T | 5_prime_UTR_variant | Exon 1 of 15 | NP_001304650.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152136Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000152 AC: 2AN: 131380Hom.: 0 AF XY: 0.0000133 AC XY: 1AN XY: 74940
GnomAD4 exome AF: 0.00000219 AC: 3AN: 1367890Hom.: 0 Cov.: 31 AF XY: 0.00000148 AC XY: 1AN XY: 676386
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.49A>T (p.S17C) alteration is located in exon 1 (coding exon 1) of the LRWD1 gene. This alteration results from a A to T substitution at nucleotide position 49, causing the serine (S) at amino acid position 17 to be replaced by a cysteine (C). 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