dbSNP rs308925: NUDT7:p.Arg100His (chr16-77735937-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001105663.3(NUDT7):c.299G>A(p.Arg100His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,613,266 control chromosomes in the GnomAD database, including 30,743 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.18 ( 2686 hom., cov: 31)

Exomes 𝑓: 0.19 ( 28057 hom. )

Consequence

NUDT7
NM_001105663.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.38

Variant links:

Genes affected

NUDT7 (HGNC:8054): (nudix hydrolase 7) The protein encoded by this gene is a member of the Nudix hydrolase family. Nudix hydrolases eliminate potentially toxic nucleotide metabolites from the cell and regulate the concentrations and availability of many different nucleotide substrates, cofactors, and signaling molecules. Alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

NUDT7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.383857E-4).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUDT7	NM_001105663.3 link	c.299G>A	p.Arg100His	missense_variant	Exon 3 of 4	ENST00000268533.9	NP_001099133.1	P0C024-1
NUDT7	NM_001243657.2 link	c.299G>A	p.Arg100His	missense_variant	Exon 3 of 5		NP_001230586.1	P0C024-3
NUDT7	NM_001243660.2 link	c.303+430G>A		intron_variant	Intron 3 of 3		NP_001230589.1	P0C024A0A087WVP7
NUDT7	NM_001243661.2 link	c.190-5645G>A		intron_variant	Intron 2 of 2		NP_001230590.1	P0C024-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUDT7	ENST00000268533.9 link	c.299G>A	p.Arg100His	missense_variant	Exon 3 of 4	1	NM_001105663.3	ENSP00000268533.5		P0C024-1

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27263

AN:

151844

Hom.:

2686

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.266

Gnomad SAS

AF:

0.332

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.236

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.179

GnomAD3 exomes

AF:

0.213

AC:

53105

AN:

249544

Hom.:

6155

AF XY:

0.219

AC XY:

29596

AN XY:

135392

show subpopulations

Gnomad AFR exome

AF:

0.122

Gnomad AMR exome

AF:

0.220

Gnomad ASJ exome

AF:

0.188

Gnomad EAS exome

AF:

0.246

Gnomad SAS exome

AF:

0.311

Gnomad FIN exome

AF:

0.263

Gnomad NFE exome

AF:

0.184

Gnomad OTH exome

AF:

0.213

GnomAD4 exome

AF:

0.189

AC:

275657

AN:

1461304

Hom.:

28057

Cov.:

AF XY:

0.192

AC XY:

139783

AN XY:

726990

show subpopulations

Gnomad4 AFR exome

AF:

0.118

Gnomad4 AMR exome

AF:

0.219

Gnomad4 ASJ exome

AF:

0.188

Gnomad4 EAS exome

AF:

0.280

Gnomad4 SAS exome

AF:

0.307

Gnomad4 FIN exome

AF:

0.265

Gnomad4 NFE exome

AF:

0.173

Gnomad4 OTH exome

AF:

0.193

GnomAD4 genome

AF:

0.179

AC:

27264

AN:

151962

Hom.:

2686

Cov.:

AF XY:

0.186

AC XY:

13838

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.122

Gnomad4 AMR

AF:

0.209

Gnomad4 ASJ

AF:

0.181

Gnomad4 EAS

AF:

0.265

Gnomad4 SAS

AF:

0.331

Gnomad4 FIN

AF:

0.274

Gnomad4 NFE

AF:

0.176

Gnomad4 OTH

AF:

0.181

Alfa

AF:

0.182

Hom.:

6881

Bravo

AF:

0.168

TwinsUK

AF:

0.175

AC:

650

ALSPAC

AF:

0.173

AC:

666

ESP6500AA

AF:

0.116

AC:

473

ESP6500EA

AF:

0.168

AC:

1410

ExAC

AF:

0.211

AC:

25513

Asia WGS

AF:

0.304

AC:

1055

AN:

3478

EpiCase

AF:

0.182

EpiControl

AF:

0.185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.062

BayesDel_addAF

Benign

-0.86

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.0050

DANN

Benign

0.88

DEOGEN2

Benign

0.015

.;T;.

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.011

LIST_S2

Benign

0.83

T;T;T

MetaRNN

Benign

0.00094

T;T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

0.33

N;N;.

PrimateAI

Benign

0.18

PROVEAN

Benign

0.87

N;N;N

REVEL

Benign

0.050

Sift

Benign

0.53

T;T;T

Sift4G

Benign

0.19

T;T;T

Polyphen

0.0020

.;B;.

Vest4

0.015

MPC

0.016

ClinPred

0.0021

GERP RS

-3.4

Varity_R

0.093

gMVP

0.41

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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