12-55721227-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_002905.5(RDH5):c.43C>T(p.Leu15Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
RDH5
NM_002905.5 synonymous
NM_002905.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.498
Genes affected
RDH5 (HGNC:9940): (retinol dehydrogenase 5) This gene encodes an enzyme belonging to the short-chain dehydrogenases/reductases (SDR) family. This retinol dehydrogenase functions to catalyze the final step in the biosynthesis of 11-cis retinaldehyde, which is the universal chromophore of visual pigments. Mutations in this gene cause autosomal recessive fundus albipunctatus, a rare form of night blindness that is characterized by a delay in the regeneration of cone and rod photopigments. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the neighboring upstream BLOC1S1 (biogenesis of lysosomal organelles complex-1, subunit 1) gene. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 12-55721227-C-T is Benign according to our data. Variant chr12-55721227-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1666978.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RDH5 | NM_002905.5 | c.43C>T | p.Leu15Leu | synonymous_variant | Exon 2 of 5 | ENST00000257895.10 | NP_002896.2 | |
RDH5 | NM_001199771.3 | c.43C>T | p.Leu15Leu | synonymous_variant | Exon 2 of 5 | NP_001186700.1 | ||
BLOC1S1-RDH5 | NR_037658.1 | n.370-462C>T | intron_variant | Intron 3 of 5 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250930Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135752
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GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461730Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727162
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Dec 15, 2021
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 14
Find out detailed SpliceAI scores and Pangolin per-transcript scores at