1-163355398-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145697.3(NUF2):c.1324G>A(p.Glu442Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000373 in 1,606,580 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 (★).
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.1324G>A | p.Glu442Lys | missense_variant | 14/14 | ENST00000271452.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUF2 | ENST00000271452.8 | c.1324G>A | p.Glu442Lys | missense_variant | 14/14 | 1 | NM_145697.3 | P1 | |
NUF2 | ENST00000367900.7 | c.1324G>A | p.Glu442Lys | missense_variant | 14/14 | 1 | P1 | ||
NUF2 | ENST00000524800.5 | c.1183G>A | p.Glu395Lys | missense_variant | 13/13 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249190Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134820
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1454412Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 723764
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.1324G>A (p.E442K) alteration is located in exon 14 (coding exon 13) of the NUF2 gene. This alteration results from a G to A substitution at nucleotide position 1324, causing the glutamic acid (E) at amino acid position 442 to be replaced by a lysine (K). 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