Variant rs10883841 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001351169.2(NT5C2):c.7A>G(p.Thr3Ala) variant causes a missense change. The variant allele was found at a frequency of 0.128 in 1,597,198 control chromosomes in the GnomAD database, including 14,609 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1139 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13470 hom. )

Consequence

NT5C2
NM_001351169.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 5.62

Variant links:

Genes affected

NT5C2 (HGNC:8022): (5'-nucleotidase, cytosolic II) This gene encodes a hydrolase that serves as an important role in cellular purine metabolism by acting primarily on inosine 5'-monophosphate and other purine nucleotides. [provided by RefSeq, Oct 2011]

NT5C2 links:

NT5C2 (HGNC:):

NT5C2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016233623).

BP6

Variant 10-103174952-T-C is Benign according to our data. Variant chr10-103174952-T-C is described in ClinVar as [Benign]. Clinvar id is 380851.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-103174952-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5C2	NM_001351169.2 linkuse as main transcript	c.7A>G	p.Thr3Ala	missense_variant	3/19	ENST00000404739.8	NP_001338098.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C2	ENST00000404739.8 linkuse as main transcript	c.7A>G	p.Thr3Ala	missense_variant	3/19	1	NM_001351169.2	ENSP00000383960.3		P49902-1

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16318

AN:

152084

Hom.:

1138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0314

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.0850

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.140

Gnomad SAS

AF:

0.0417

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.119

GnomAD3 exomes

AF:

0.118

AC:

29236

AN:

247866

Hom.:

2013

AF XY:

0.118

AC XY:

15854

AN XY:

133970

show subpopulations

Gnomad AFR exome

AF:

0.0302

Gnomad AMR exome

AF:

0.0805

Gnomad ASJ exome

AF:

0.151

Gnomad EAS exome

AF:

0.147

Gnomad SAS exome

AF:

0.0391

Gnomad FIN exome

AF:

0.158

Gnomad NFE exome

AF:

0.147

Gnomad OTH exome

AF:

0.128

GnomAD4 exome

AF:

0.130

AC:

187668

AN:

1444996

Hom.:

13470

Cov.:

AF XY:

0.128

AC XY:

92065

AN XY:

719810

show subpopulations

Gnomad4 AFR exome

AF:

0.0255

Gnomad4 AMR exome

AF:

0.0801

Gnomad4 ASJ exome

AF:

0.150

Gnomad4 EAS exome

AF:

0.0969

Gnomad4 SAS exome

AF:

0.0386

Gnomad4 FIN exome

AF:

0.155

Gnomad4 NFE exome

AF:

0.142

Gnomad4 OTH exome

AF:

0.126

GnomAD4 genome

AF:

0.107

AC:

16314

AN:

152202

Hom.:

1139

Cov.:

AF XY:

0.106

AC XY:

7871

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.0313

Gnomad4 AMR

AF:

0.0848

Gnomad4 ASJ

AF:

0.156

Gnomad4 EAS

AF:

0.139

Gnomad4 SAS

AF:

0.0422

Gnomad4 FIN

AF:

0.155

Gnomad4 NFE

AF:

0.151

Gnomad4 OTH

AF:

0.120

Alfa

AF:

0.136

Hom.:

3684

Bravo

AF:

0.0993

TwinsUK

AF:

0.137

AC:

509

ALSPAC

AF:

0.133

AC:

512

ESP6500AA

AF:

0.0340

AC:

150

ESP6500EA

AF:

0.149

AC:

1282

ExAC

AF:

0.114

AC:

13808

Asia WGS

AF:

0.0700

AC:

242

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 01, 2016

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Hereditary spastic paraplegia 45

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.061

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.12

T;T;.

Eigen

Benign

-0.10

Eigen_PC

Benign

0.098

FATHMM_MKL

Uncertain

0.95

LIST_S2

Uncertain

0.96

.;D;D

MetaRNN

Benign

0.0016

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.69

N;N;.

PrimateAI

Uncertain

0.60

PROVEAN

Benign

-0.37

N;N;.

REVEL

Benign

0.075

Sift

Benign

0.055

T;T;.

Sift4G

Uncertain

0.051

T;T;D

Polyphen

0.0040

B;B;.

Vest4

0.17

MPC

0.68

ClinPred

0.015

GERP RS

5.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.17

gMVP

0.76

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over