rs1062492
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002452.4(NUDT1):c.*49C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,591,936 control chromosomes in the GnomAD database, including 25,184 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.15 ( 1869 hom., cov: 32)
Exomes 𝑓: 0.18 ( 23315 hom. )
Consequence
NUDT1
NM_002452.4 3_prime_UTR
NM_002452.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0370
Genes affected
NUDT1 (HGNC:8048): (nudix hydrolase 1) Misincorporation of oxidized nucleoside triphosphates into DNA/RNA during replication and transcription can cause mutations that may result in carcinogenesis or neurodegeneration. The protein encoded by this gene is an enzyme that hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP, 8-oxo-dATP, 2-hydroxy-dATP, and 2-hydroxy rATP, to monophosphates, thereby preventing misincorporation. The encoded protein is localized mainly in the cytoplasm, with some in the mitochondria, suggesting that it is involved in the sanitization of nucleotide pools both for nuclear and mitochondrial genomes. Several alternatively spliced transcript variants, some of which encode distinct isoforms, have been identified. Additional variants have been observed, but their full-length natures have not been determined. A rare single-nucleotide polymorphism that results in the production of an additional, longer isoform (p26) has been described. [provided by RefSeq, Dec 2018]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUDT1 | NM_002452.4 | c.*49C>T | 3_prime_UTR_variant | 4/4 | ENST00000356714.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUDT1 | ENST00000356714.6 | c.*49C>T | 3_prime_UTR_variant | 4/4 | 1 | NM_002452.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.145 AC: 22097AN: 151910Hom.: 1861 Cov.: 32
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GnomAD3 exomes AF: 0.170 AC: 42283AN: 248864Hom.: 3992 AF XY: 0.173 AC XY: 23345AN XY: 134914
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GnomAD4 exome AF: 0.176 AC: 253565AN: 1439914Hom.: 23315 Cov.: 27 AF XY: 0.177 AC XY: 126799AN XY: 717652
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GnomAD4 genome ? AF: 0.146 AC: 22126AN: 152022Hom.: 1869 Cov.: 32 AF XY: 0.145 AC XY: 10769AN XY: 74296
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at