rs766143193
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The ENST00000369846.9(LCA5):c.1676C>T(p.Ser559Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,612,640 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S559S) has been classified as Likely benign.
Frequency
Consequence
ENST00000369846.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LCA5 | NM_001122769.3 | c.1676C>T | p.Ser559Leu | missense_variant | 8/8 | ENST00000369846.9 | NP_001116241.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LCA5 | ENST00000369846.9 | c.1676C>T | p.Ser559Leu | missense_variant | 8/8 | 1 | NM_001122769.3 | ENSP00000358861 | P1 | |
LCA5 | ENST00000392959.5 | c.1676C>T | p.Ser559Leu | missense_variant | 9/9 | 1 | ENSP00000376686 | P1 | ||
ENST00000652956.1 | n.469+5982G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152040Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 249724Hom.: 0 AF XY: 0.0000519 AC XY: 7AN XY: 134992
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1460482Hom.: 0 Cov.: 33 AF XY: 0.0000248 AC XY: 18AN XY: 726548
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at