8-22109276-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024815.4(NUDT18):c.25G>A(p.Ala9Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000243 in 1,396,632 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024815.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUDT18 | ENST00000611621.2 | c.25G>A | p.Ala9Thr | missense_variant | Exon 1 of 3 | 1 | NM_024815.4 | ENSP00000480722.1 | ||
NUDT18 | ENST00000613958.1 | c.25G>A | p.Ala9Thr | missense_variant | Exon 1 of 2 | 2 | ENSP00000479883.1 |
Frequencies
GnomAD3 genomes AF: 0.00139 AC: 211AN: 151874Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000175 AC: 6AN: 34314Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 21226
GnomAD4 exome AF: 0.000103 AC: 128AN: 1244652Hom.: 0 Cov.: 32 AF XY: 0.0000820 AC XY: 50AN XY: 609906
GnomAD4 genome AF: 0.00139 AC: 211AN: 151980Hom.: 0 Cov.: 34 AF XY: 0.00136 AC XY: 101AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.25G>A (p.A9T) alteration is located in exon 1 (coding exon 1) of the NUDT18 gene. This alteration results from a G to A substitution at nucleotide position 25, causing the alanine (A) at amino acid position 9 to be replaced by a threonine (T). 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