21-39410003-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152505.4(LCA5L):c.1258G>A(p.Glu420Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000203 in 1,573,940 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 (★).
Frequency
Consequence
NM_152505.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LCA5L | ENST00000288350.8 | c.1258G>A | p.Glu420Lys | missense_variant | Exon 10 of 11 | 5 | NM_152505.4 | ENSP00000288350.3 | ||
GET1-SH3BGR | ENST00000647779.1 | c.336+18167C>T | intron_variant | Intron 3 of 8 | ENSP00000497977.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247022Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133276
GnomAD4 exome AF: 0.0000183 AC: 26AN: 1421778Hom.: 0 Cov.: 26 AF XY: 0.0000226 AC XY: 16AN XY: 709296
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1258G>A (p.E420K) alteration is located in exon 9 (coding exon 6) of the LCA5L gene. This alteration results from a G to A substitution at nucleotide position 1258, causing the glutamic acid (E) at amino acid position 420 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