5-152404656-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020167.5(NMUR2):c.458G>T(p.Arg153Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,708 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020167.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NMUR2 | ENST00000255262.4 | c.458G>T | p.Arg153Leu | missense_variant | Exon 1 of 4 | 1 | NM_020167.5 | ENSP00000255262.4 | ||
NMUR2 | ENST00000518933.1 | n.273-6512G>T | intron_variant | Intron 2 of 3 | 3 | |||||
ENSG00000286749 | ENST00000663460.1 | n.216+29443C>A | intron_variant | Intron 1 of 3 | ||||||
ENSG00000286749 | ENST00000663819.1 | n.183+29443C>A | intron_variant | Intron 1 of 3 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 151906Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000127 AC: 32AN: 251162Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135798
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461692Hom.: 0 Cov.: 34 AF XY: 0.0000138 AC XY: 10AN XY: 727156
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152016Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.458G>T (p.R153L) alteration is located in exon 1 (coding exon 1) of the NMUR2 gene. This alteration results from a G to T substitution at nucleotide position 458, causing the arginine (R) at amino acid position 153 to be replaced by a leucine (L). 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