11-76660026-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001128922.2(LRRC32):c.1567G>A(p.Glu523Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,614,024 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_001128922.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC32 | NM_001128922.2 | c.1567G>A | p.Glu523Lys | missense_variant | Exon 3 of 3 | ENST00000260061.9 | NP_001122394.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250730Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135676
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461770Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727194
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1567G>A (p.E523K) alteration is located in exon 3 (coding exon 2) of the LRRC32 gene. This alteration results from a G to A substitution at nucleotide position 1567, causing the glutamic acid (E) at amino acid position 523 to be replaced by a lysine (K). 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