NM_001351169.2:c.772-425C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001351169.2(NT5C2):​c.772-425C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0884 in 152,240 control chromosomes in the GnomAD database, including 841 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 0.088 ( 841 hom., cov: 31)

Consequence

NT5C2
NM_001351169.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.65

Publications

24 publications found
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 Gene-Disease associations (from GenCC):
  • hereditary spastic paraplegia 45
    Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NT5C2NM_001351169.2 linkc.772-425C>T intron_variant Intron 11 of 18 ENST00000404739.8 NP_001338098.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NT5C2ENST00000404739.8 linkc.772-425C>T intron_variant Intron 11 of 18 1 NM_001351169.2 ENSP00000383960.3 P49902-1

Frequencies

GnomAD3 genomes
AF:
0.0884
AC:
13449
AN:
152122
Hom.:
836
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0390
Gnomad AMI
AF:
0.0175
Gnomad AMR
AF:
0.136
Gnomad ASJ
AF:
0.0732
Gnomad EAS
AF:
0.278
Gnomad SAS
AF:
0.184
Gnomad FIN
AF:
0.0747
Gnomad MID
AF:
0.0728
Gnomad NFE
AF:
0.0901
Gnomad OTH
AF:
0.101
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0884
AC:
13465
AN:
152240
Hom.:
841
Cov.:
31
AF XY:
0.0907
AC XY:
6755
AN XY:
74436
show subpopulations
African (AFR)
AF:
0.0391
AC:
1624
AN:
41558
American (AMR)
AF:
0.136
AC:
2080
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.0732
AC:
254
AN:
3472
East Asian (EAS)
AF:
0.278
AC:
1443
AN:
5186
South Asian (SAS)
AF:
0.184
AC:
887
AN:
4828
European-Finnish (FIN)
AF:
0.0747
AC:
790
AN:
10582
Middle Eastern (MID)
AF:
0.0714
AC:
21
AN:
294
European-Non Finnish (NFE)
AF:
0.0902
AC:
6132
AN:
68002
Other (OTH)
AF:
0.103
AC:
218
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
600
1200
1800
2400
3000
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
162
324
486
648
810
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0682
Hom.:
108
Bravo
AF:
0.0911
Asia WGS
AF:
0.195
AC:
676
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.21
DANN
Benign
0.71
PhyloP100
-1.6
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs12412038; hg19: chr10-104856162; API