2-18555715-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_020905.4(RDH14):c.487G>A(p.Val163Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020905.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RDH14 | NM_020905.4 | c.487G>A | p.Val163Met | missense_variant | Exon 2 of 2 | ENST00000381249.4 | NP_065956.1 | |
NT5C1B-RDH14 | NM_001199103.2 | c.1429G>A | p.Val477Met | missense_variant | Exon 9 of 9 | NP_001186032.1 | ||
NT5C1B-RDH14 | NM_001199104.2 | c.*69G>A | 3_prime_UTR_variant | Exon 11 of 11 | NP_001186033.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RDH14 | ENST00000381249.4 | c.487G>A | p.Val163Met | missense_variant | Exon 2 of 2 | 1 | NM_020905.4 | ENSP00000370648.3 | ||
NT5C1B-RDH14 | ENST00000532967 | c.*69G>A | 3_prime_UTR_variant | Exon 11 of 11 | 2 | ENSP00000433415.1 | ||||
NT5C1B-RDH14 | ENST00000444297.2 | c.1429G>A | p.Val477Met | missense_variant | Exon 9 of 9 | 2 | ENSP00000412639.2 | |||
RDH14 | ENST00000468071.1 | n.144G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.487G>A (p.V163M) alteration is located in exon 2 (coding exon 2) of the RDH14 gene. This alteration results from a G to A substitution at nucleotide position 487, causing the valine (V) at amino acid position 163 to be replaced by a methionine (M). 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
Publications
No publications associated with this variant yet.