chr11-67628995-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001243750.2(NUDT8):c.251G>A(p.Arg84Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,612,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001243750.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUDT8 | ENST00000376693.3 | c.251G>A | p.Arg84Gln | missense_variant | Exon 2 of 4 | 2 | NM_001243750.2 | ENSP00000365883.2 | ||
NUDT8 | ENST00000301490.8 | c.251G>A | p.Arg84Gln | missense_variant | Exon 2 of 3 | 1 | ENSP00000301490.4 | |||
NUDT8 | ENST00000534054.1 | n.927G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152258Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250080Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135548
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460644Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726612
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.251G>A (p.R84Q) alteration is located in exon 2 (coding exon 2) of the NUDT8 gene. This alteration results from a G to A substitution at nucleotide position 251, causing the arginine (R) at amino acid position 84 to be replaced by a glutamine (Q). 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