14-67729195-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152443.3(RDH12):c.663C>A(p.Thr221Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152443.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RDH12 | NM_152443.3 | c.663C>A | p.Thr221Thr | synonymous_variant | Exon 8 of 9 | ENST00000551171.6 | NP_689656.2 | |
RDH12 | XM_047430965.1 | c.663C>A | p.Thr221Thr | synonymous_variant | Exon 8 of 9 | XP_047286921.1 | ||
ZFYVE26 | XM_047431173.1 | c.*547G>T | 3_prime_UTR_variant | Exon 42 of 42 | XP_047287129.1 | |||
GPHN | XM_047430879.1 | c.1313-6000C>A | intron_variant | Intron 14 of 14 | XP_047286835.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RDH12 | ENST00000551171.6 | c.663C>A | p.Thr221Thr | synonymous_variant | Exon 8 of 9 | 1 | NM_152443.3 | ENSP00000449079.1 | ||
RDH12 | ENST00000267502.3 | c.663C>A | p.Thr221Thr | synonymous_variant | Exon 7 of 8 | 5 | ENSP00000267502.3 | |||
RDH12 | ENST00000552873.1 | n.32C>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 5 | |||||
ZFYVE26 | ENST00000394455.6 | n.3288+16G>T | intron_variant | Intron 14 of 14 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Leber congenital amaurosis 13 Uncertain:1
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with RDH12-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects codon 221 of the RDH12 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the RDH12 protein. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.