11-64229320-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_032344.4(NUDT22):āc.653G>Cā(p.Arg218Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000348 in 1,610,318 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R218Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_032344.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUDT22 | NM_032344.4 | c.653G>C | p.Arg218Pro | missense_variant | 4/6 | ENST00000279206.8 | |
LOC124902687 | XR_007062713.1 | n.921C>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUDT22 | ENST00000279206.8 | c.653G>C | p.Arg218Pro | missense_variant | 4/6 | 1 | NM_032344.4 | P1 | |
ENST00000534988.1 | n.817C>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000206 AC: 5AN: 242740Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131600
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1458076Hom.: 0 Cov.: 32 AF XY: 0.0000386 AC XY: 28AN XY: 725018
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.653G>C (p.R218P) alteration is located in exon 4 (coding exon 3) of the NUDT22 gene. This alteration results from a G to C substitution at nucleotide position 653, causing the arginine (R) at amino acid position 218 to be replaced by a proline (P). 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