1-163355367-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145697.3(NUF2):āc.1293G>Cā(p.Glu431Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000935 in 1,604,506 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_145697.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUF2 | NM_145697.3 | c.1293G>C | p.Glu431Asp | missense_variant | 14/14 | ENST00000271452.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUF2 | ENST00000271452.8 | c.1293G>C | p.Glu431Asp | missense_variant | 14/14 | 1 | NM_145697.3 | P1 | |
NUF2 | ENST00000367900.7 | c.1293G>C | p.Glu431Asp | missense_variant | 14/14 | 1 | P1 | ||
NUF2 | ENST00000524800.5 | c.1152G>C | p.Glu384Asp | missense_variant | 13/13 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000163 AC: 4AN: 245954Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133164
GnomAD4 exome AF: 0.00000413 AC: 6AN: 1452398Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 722584
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 01, 2022 | The c.1293G>C (p.E431D) alteration is located in exon 14 (coding exon 13) of the NUF2 gene. This alteration results from a G to C substitution at nucleotide position 1293, causing the glutamic acid (E) at amino acid position 431 to be replaced by an aspartic acid (D). 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