1-163336816-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_145697.3(NUF2):c.403C>T(p.Arg135Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000155 in 1,612,066 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R135H) has been classified as Uncertain significance.
Frequency
Consequence
NM_145697.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUF2 | NM_145697.3 | c.403C>T | p.Arg135Cys | missense_variant | 6/14 | ENST00000271452.8 | NP_663735.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUF2 | ENST00000271452.8 | c.403C>T | p.Arg135Cys | missense_variant | 6/14 | 1 | NM_145697.3 | ENSP00000271452.3 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151978Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251126Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135722
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1460088Hom.: 0 Cov.: 29 AF XY: 0.0000165 AC XY: 12AN XY: 726464
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151978Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74220
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2021 | The c.403C>T (p.R135C) alteration is located in exon 6 (coding exon 5) of the NUF2 gene. This alteration results from a C to T substitution at nucleotide position 403, causing the arginine (R) at amino acid position 135 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