5-6599940-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017755.6(NSUN2):c.2290C>A(p.His764Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,612,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017755.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NSUN2 | NM_017755.6 | c.2290C>A | p.His764Asn | missense_variant | Exon 19 of 19 | ENST00000264670.11 | NP_060225.4 | |
NSUN2 | NM_001193455.2 | c.2185C>A | p.His729Asn | missense_variant | Exon 18 of 18 | NP_001180384.1 | ||
NSUN2 | NR_037947.2 | n.2270C>A | non_coding_transcript_exon_variant | Exon 18 of 18 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251046Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135690
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1460620Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726612
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74388
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces histidine, which is basic and polar, with asparagine, which is neutral and polar, at codon 764 of the NSUN2 protein (p.His764Asn). This variant is present in population databases (rs767318342, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with NSUN2-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at