rs732998

Variant summary

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

The NM_001351169.2(NT5C2):​c.175+1262A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0943 in 152,200 control chromosomes in the GnomAD database, including 889 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 0.094 ( 889 hom., cov: 32)

Consequence

NT5C2
NM_001351169.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308
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]

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 (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NT5C2NM_001351169.2 linkuse as main transcriptc.175+1262A>G intron_variant ENST00000404739.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NT5C2ENST00000404739.8 linkuse as main transcriptc.175+1262A>G intron_variant 1 NM_001351169.2 P1P49902-1

Frequencies

GnomAD3 genomes
AF:
0.0943
AC:
14339
AN:
152082
Hom.:
883
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0594
Gnomad AMI
AF:
0.0175
Gnomad AMR
AF:
0.138
Gnomad ASJ
AF:
0.0732
Gnomad EAS
AF:
0.277
Gnomad SAS
AF:
0.184
Gnomad FIN
AF:
0.0745
Gnomad MID
AF:
0.0728
Gnomad NFE
AF:
0.0904
Gnomad OTH
AF:
0.103
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0943
AC:
14359
AN:
152200
Hom.:
889
Cov.:
32
AF XY:
0.0962
AC XY:
7162
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.0595
Gnomad4 AMR
AF:
0.138
Gnomad4 ASJ
AF:
0.0732
Gnomad4 EAS
AF:
0.277
Gnomad4 SAS
AF:
0.183
Gnomad4 FIN
AF:
0.0745
Gnomad4 NFE
AF:
0.0905
Gnomad4 OTH
AF:
0.106
Alfa
AF:
0.0689
Hom.:
120
Bravo
AF:
0.0981
Asia WGS
AF:
0.196
AC:
680
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
4.1
DANN
Benign
0.66

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.

Other links and lift over

dbSNP: rs732998; hg19: chr10-104897901; API