2-54987537-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020532.5(RTN4):c.3175G>T(p.Gly1059Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000359 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020532.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RTN4 | NM_020532.5 | c.3175G>T | p.Gly1059Cys | missense_variant | Exon 4 of 9 | ENST00000337526.11 | NP_065393.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251304Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135842
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461856Hom.: 0 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 727230
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152110Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3175G>T (p.G1059C) alteration is located in exon 4 (coding exon 4) of the RTN4 gene. This alteration results from a G to T substitution at nucleotide position 3175, causing the glycine (G) at amino acid position 1059 to be replaced by a cysteine (C). 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