chr1-163347853-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.1039G>A(p.Val347Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,612,086 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.1039G>A | p.Val347Met | missense_variant | 12/14 | ENST00000271452.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUF2 | ENST00000271452.8 | c.1039G>A | p.Val347Met | missense_variant | 12/14 | 1 | NM_145697.3 | P1 | |
NUF2 | ENST00000367900.7 | c.1039G>A | p.Val347Met | missense_variant | 12/14 | 1 | P1 | ||
NUF2 | ENST00000524800.5 | c.898G>A | p.Val300Met | missense_variant | 11/13 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249716Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134946
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459922Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726200
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2023 | The c.1039G>A (p.V347M) alteration is located in exon 12 (coding exon 11) of the NUF2 gene. This alteration results from a G to A substitution at nucleotide position 1039, causing the valine (V) at amino acid position 347 to be replaced by a methionine (M). 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