Variant rs6686 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_014142.4(NUDT5):c.609A>G(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: 𝑓 0.47 ( 17235 hom., cov: 32)

Exomes 𝑓: 0.50 ( 182390 hom. )

Consequence

NUDT5
NM_014142.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.91

Variant links:

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]

NUDT5 links:

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]

SEC61A2 links:

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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	Protein	UniProt
NUDT5	NM_014142.4 linkuse as main transcript	c.609A>G	p.Ala203=	synonymous_variant	10/10	ENST00000491614.6	NP_054861.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUDT5	ENST00000491614.6 linkuse as main transcript	c.609A>G	p.Ala203=	synonymous_variant	10/10	1	NM_014142.4	ENSP00000419628	P1

Frequencies

GnomAD3 genomes

AF:

0.474

AC:

72034

AN:

151968

Hom.:

17230

Cov.:

show subpopulations

Gnomad AFR

AF:

0.448

Gnomad AMI

AF:

0.350

Gnomad AMR

AF:

0.443

Gnomad ASJ

AF:

0.451

Gnomad EAS

AF:

0.554

Gnomad SAS

AF:

0.369

Gnomad FIN

AF:

0.439

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.445

GnomAD3 exomes

AF:

0.479

AC:

120251

AN:

251250

Hom.:

29354

AF XY:

0.470

AC XY:

63832

AN XY:

135800

show subpopulations

Gnomad AFR exome

AF:

0.444

Gnomad AMR exome

AF:

0.512

Gnomad ASJ exome

AF:

0.446

Gnomad EAS exome

AF:

0.559

Gnomad SAS exome

AF:

0.360

Gnomad FIN exome

AF:

0.440

Gnomad NFE exome

AF:

0.503

Gnomad OTH exome

AF:

0.476

GnomAD4 exome

AF:

0.497

AC:

726141

AN:

1461578

Hom.:

182390

Cov.:

AF XY:

0.493

AC XY:

358143

AN XY:

727088

show subpopulations

Gnomad4 AFR exome

AF:

0.441

Gnomad4 AMR exome

AF:

0.509

Gnomad4 ASJ exome

AF:

0.448

Gnomad4 EAS exome

AF:

0.546

Gnomad4 SAS exome

AF:

0.362

Gnomad4 FIN exome

AF:

0.436

Gnomad4 NFE exome

AF:

0.512

Gnomad4 OTH exome

AF:

0.482

GnomAD4 genome

AF:

0.474

AC:

72058

AN:

152086

Hom.:

17235

Cov.:

AF XY:

0.466

AC XY:

34651

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.447

Gnomad4 AMR

AF:

0.443

Gnomad4 ASJ

AF:

0.451

Gnomad4 EAS

AF:

0.554

Gnomad4 SAS

AF:

0.367

Gnomad4 FIN

AF:

0.439

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.439

Alfa

AF:

0.489

Hom.:

15150

Bravo

AF:

0.478

Asia WGS

AF:

0.403

AC:

1405

AN:

3478

EpiCase

AF:

0.488

EpiControl

AF:

0.483

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.23

DANN

Benign

0.43

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over