4-122893210-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_007083.5(NUDT6):c.569G>A(p.Arg190Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000156 in 1,606,722 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_007083.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUDT6 | NM_007083.5 | c.569G>A | p.Arg190Gln | missense_variant | Exon 5 of 5 | ENST00000304430.10 | NP_009014.2 | |
FGF2 | NM_001361665.2 | c.*814C>T | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000644866.2 | NP_001348594.1 | ||
NUDT6 | NM_198041.3 | c.62G>A | p.Arg21Gln | missense_variant | Exon 5 of 5 | NP_932158.1 | ||
FGF2 | NM_002006.6 | c.*814C>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.569G>A | p.Arg190Gln | missense_variant | Exon 5 of 5 | 1 | NM_007083.5 | ENSP00000306070.5 | ||
FGF2 | ENST00000644866.2 | c.*814C>T | 3_prime_UTR_variant | Exon 3 of 3 | NM_001361665.2 | ENSP00000494222.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247156Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133778
GnomAD4 exome AF: 0.0000165 AC: 24AN: 1454590Hom.: 0 Cov.: 31 AF XY: 0.0000180 AC XY: 13AN XY: 722284
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.569G>A (p.R190Q) 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 569, causing the arginine (R) at amino acid position 190 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