7-102467788-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152892.3(LRWD1):āc.643A>Cā(p.Lys215Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000172 in 1,551,014 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.643A>C | p.Lys215Gln | missense_variant | Exon 5 of 15 | ENST00000292616.10 | NP_690852.1 | |
LRWD1 | NM_001317721.2 | c.187A>C | p.Lys63Gln | missense_variant | Exon 5 of 15 | NP_001304650.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000134 AC: 21AN: 156490Hom.: 0 AF XY: 0.0000727 AC XY: 6AN XY: 82488
GnomAD4 exome AF: 0.000177 AC: 247AN: 1398890Hom.: 0 Cov.: 33 AF XY: 0.000183 AC XY: 126AN XY: 689992
GnomAD4 genome AF: 0.000125 AC: 19AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.643A>C (p.K215Q) alteration is located in exon 5 (coding exon 5) of the LRWD1 gene. This alteration results from a A to C substitution at nucleotide position 643, causing the lysine (K) at amino acid position 215 to be replaced by a glutamine (Q). 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