4-122892920-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007083.5(NUDT6):c.859G>A(p.Glu287Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,016 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_007083.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUDT6 | NM_007083.5 | c.859G>A | p.Glu287Lys | missense_variant | Exon 5 of 5 | ENST00000304430.10 | NP_009014.2 | |
FGF2 | NM_001361665.2 | c.*524C>T | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000644866.2 | NP_001348594.1 | ||
NUDT6 | NM_198041.3 | c.352G>A | p.Glu118Lys | missense_variant | Exon 5 of 5 | NP_932158.1 | ||
FGF2 | NM_002006.6 | c.*524C>T | 3_prime_UTR_variant | Exon 3 of 3 | NP_001997.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUDT6 | ENST00000304430.10 | c.859G>A | p.Glu287Lys | missense_variant | Exon 5 of 5 | 1 | NM_007083.5 | ENSP00000306070.5 | ||
FGF2 | ENST00000644866.2 | c.*524C>T | 3_prime_UTR_variant | Exon 3 of 3 | NM_001361665.2 | ENSP00000494222.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152016Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152016Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.859G>A (p.E287K) alteration is located in exon 5 (coding exon 5) of the NUDT6 gene. This alteration results from a G to A substitution at nucleotide position 859, causing the glutamic acid (E) at amino acid position 287 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