rs11788425
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001161.5(NUDT2):c.-264-2372A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,952 control chromosomes in the GnomAD database, including 10,785 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 0.35 ( 10785 hom., cov: 31)
Consequence
NUDT2
NM_001161.5 intron
NM_001161.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.194
Genes affected
NUDT2 (HGNC:8049): (nudix hydrolase 2) This gene encodes a member of the MutT family of nucleotide pyrophosphatases, a subset of the larger NUDIX hydrolase family. The gene product possesses a modification of the MutT sequence motif found in certain nucleotide pyrophosphatases. The enzyme asymmetrically hydrolyzes Ap4A to yield AMP and ATP and is responsible for maintaining the intracellular level of the dinucleotide Ap4A, the function of which has yet to be established. This gene may be a candidate tumor suppressor gene. Alternative splicing has been observed at this locus and four transcript variants, all encoding the same protein, have been identified. [provided by RefSeq, Sep 2011]
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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=-0.8).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUDT2 | NM_001161.5 | c.-264-2372A>G | intron_variant | ENST00000379158.7 | |||
NUDT2 | NM_001244390.2 | c.-17+4258A>G | intron_variant | ||||
NUDT2 | NM_147172.3 | c.-193-2443A>G | intron_variant | ||||
NUDT2 | NM_147173.3 | c.-152+4258A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUDT2 | ENST00000379158.7 | c.-264-2372A>G | intron_variant | 3 | NM_001161.5 | P1 | |||
NUDT2 | ENST00000346365.8 | c.-152+4258A>G | intron_variant | 1 | P1 | ||||
NUDT2 | ENST00000379155.9 | c.-193-2443A>G | intron_variant | 3 | P1 | ||||
NUDT2 | ENST00000618590.1 | c.-17+4258A>G | intron_variant | 3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.351 AC: 53234AN: 151834Hom.: 10780 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.350 AC: 53247AN: 151952Hom.: 10785 Cov.: 31 AF XY: 0.353 AC XY: 26202AN XY: 74288
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74288
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1560
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at