rs6686
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_014142.4(NUDT5):āc.609A>Gā(p.Ala203=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 1,613,664 control chromosomes in the GnomAD database, including 199,625 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: š 0.47 ( 17235 hom., cov: 32)
Exomes š: 0.50 ( 182390 hom. )
Consequence
NUDT5
NM_014142.4 synonymous
NM_014142.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.91
Genes affected
NUDT5 (HGNC:8052): (nudix hydrolase 5) This gene belongs to the Nudix (nucleoside diphosphate linked moiety X) hydrolase superfamily. The encoded enzyme catalyzes the hydrolysis of modified nucleoside diphosphates, including ADP-ribose (ADPR) and 8-oxoGua-containing 8-oxo-dADP and 8-oxo-dGDP. Protein-bound ADP ribose can be hazardous to the cell because it can modify some amino acid residues, resulting in the inhibition of ATP-activated potassium channels. 8-oxoGua is an oxidized form of guanine that can potentially alter genetic information by pairing with adenine and cytosine in RNA. Presence of 8-oxoGua in RNA results in formation of abnormal proteins due to translational errors. [provided by RefSeq, Aug 2013]
SEC61A2 (HGNC:17702): (SEC61 translocon subunit alpha 2) The protein encoded by this gene has similarity to a mouse protein which suggests a role in the insertion of secretory and membrane polypeptides into the endoplasmic reticulum. It may also be required for the assembly of membrane and secretory proteins. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP7
?
Synonymous conserved (PhyloP=-4.91 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUDT5 | NM_014142.4 | c.609A>G | p.Ala203= | synonymous_variant | 10/10 | ENST00000491614.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUDT5 | ENST00000491614.6 | c.609A>G | p.Ala203= | synonymous_variant | 10/10 | 1 | NM_014142.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.474 AC: 72034AN: 151968Hom.: 17230 Cov.: 32
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GnomAD3 exomes AF: 0.479 AC: 120251AN: 251250Hom.: 29354 AF XY: 0.470 AC XY: 63832AN XY: 135800
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GnomAD4 exome AF: 0.497 AC: 726141AN: 1461578Hom.: 182390 Cov.: 56 AF XY: 0.493 AC XY: 358143AN XY: 727088
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GnomAD4 genome ? AF: 0.474 AC: 72058AN: 152086Hom.: 17235 Cov.: 32 AF XY: 0.466 AC XY: 34651AN XY: 74340
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at