Variant chr7-2250887-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002452.4(NUDT1):c.357C>T(p.Asp119=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 1,613,992 control chromosomes in the GnomAD database, including 27,388 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 0.16 ( 2166 hom., cov: 32)

Exomes 𝑓: 0.18 ( 25222 hom. )

Consequence

NUDT1
NM_002452.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.139

Variant links:

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]

NUDT1 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=-0.56).

BP7

Synonymous conserved (PhyloP=-0.139 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUDT1	NM_002452.4 linkuse as main transcript	c.357C>T	p.Asp119=	synonymous_variant	4/4	ENST00000356714.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUDT1	ENST00000356714.6 linkuse as main transcript	c.357C>T	p.Asp119=	synonymous_variant	4/4	1	NM_002452.4	P1	P36639-4

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24857

AN:

152104

Hom.:

2157

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.0634

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.186

Gnomad OTH

AF:

0.200

GnomAD3 exomes

AF:

0.178

AC:

44754

AN:

251486

Hom.:

4365

AF XY:

0.180

AC XY:

24524

AN XY:

135920

show subpopulations

Gnomad AFR exome

AF:

0.111

Gnomad AMR exome

AF:

0.194

Gnomad ASJ exome

AF:

0.242

Gnomad EAS exome

AF:

0.0592

Gnomad SAS exome

AF:

0.194

Gnomad FIN exome

AF:

0.160

Gnomad NFE exome

AF:

0.194

Gnomad OTH exome

AF:

0.200

GnomAD4 exome

AF:

0.182

AC:

266565

AN:

1461770

Hom.:

25222

Cov.:

AF XY:

0.183

AC XY:

132920

AN XY:

727192

show subpopulations

Gnomad4 AFR exome

AF:

0.106

Gnomad4 AMR exome

AF:

0.195

Gnomad4 ASJ exome

AF:

0.242

Gnomad4 EAS exome

AF:

0.0510

Gnomad4 SAS exome

AF:

0.187

Gnomad4 FIN exome

AF:

0.159

Gnomad4 NFE exome

AF:

0.187

Gnomad4 OTH exome

AF:

0.186

GnomAD4 genome

AF:

0.164

AC:

24892

AN:

152222

Hom.:

2166

Cov.:

AF XY:

0.163

AC XY:

12105

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.109

Gnomad4 AMR

AF:

0.212

Gnomad4 ASJ

AF:

0.247

Gnomad4 EAS

AF:

0.0628

Gnomad4 SAS

AF:

0.206

Gnomad4 FIN

AF:

0.151

Gnomad4 NFE

AF:

0.186

Gnomad4 OTH

AF:

0.198

Alfa

AF:

0.187

Hom.:

3816

Bravo

AF:

0.167

Asia WGS

AF:

0.145

AC:

505

AN:

3478

EpiCase

AF:

0.193

EpiControl

AF:

0.199

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

0.49

DANN

Benign

0.62

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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