rs2295890

Variant summary

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

The ENST00000369651(NT5E):​c.-396G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 213,556 control chromosomes in the GnomAD database, including 3,697 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 0.18 ( 3053 hom., cov: 32)
Exomes 𝑓: 0.13 ( 644 hom. )

Consequence

NT5E
ENST00000369651 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.17
Variant links:
Genes affected
NT5E (HGNC:8021): (5'-nucleotidase ecto) The protein encoded by this gene is a plasma membrane protein that catalyzes the conversion of extracellular nucleotides to membrane-permeable nucleosides. The encoded protein is used as a determinant of lymphocyte differentiation. Defects in this gene can lead to the calcification of joints and arteries. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NT5EENST00000369651 linkc.-396G>C 5_prime_UTR_variant Exon 1 of 8 2 ENSP00000358665.3 P21589-2

Frequencies

GnomAD3 genomes
AF:
0.184
AC:
28031
AN:
152104
Hom.:
3052
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.303
Gnomad AMI
AF:
0.135
Gnomad AMR
AF:
0.132
Gnomad ASJ
AF:
0.160
Gnomad EAS
AF:
0.0616
Gnomad SAS
AF:
0.169
Gnomad FIN
AF:
0.106
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.149
Gnomad OTH
AF:
0.166
GnomAD4 exome
AF:
0.130
AC:
7950
AN:
61332
Hom.:
644
Cov.:
0
AF XY:
0.130
AC XY:
3950
AN XY:
30490
show subpopulations
Gnomad4 AFR exome
AF:
0.278
Gnomad4 AMR exome
AF:
0.0994
Gnomad4 ASJ exome
AF:
0.145
Gnomad4 EAS exome
AF:
0.0486
Gnomad4 SAS exome
AF:
0.151
Gnomad4 FIN exome
AF:
0.0915
Gnomad4 NFE exome
AF:
0.129
Gnomad4 OTH exome
AF:
0.136
GnomAD4 genome
AF:
0.184
AC:
28054
AN:
152224
Hom.:
3053
Cov.:
32
AF XY:
0.179
AC XY:
13349
AN XY:
74442
show subpopulations
Gnomad4 AFR
AF:
0.303
Gnomad4 AMR
AF:
0.132
Gnomad4 ASJ
AF:
0.160
Gnomad4 EAS
AF:
0.0616
Gnomad4 SAS
AF:
0.168
Gnomad4 FIN
AF:
0.106
Gnomad4 NFE
AF:
0.149
Gnomad4 OTH
AF:
0.166
Alfa
AF:
0.165
Hom.:
322
Bravo
AF:
0.189
Asia WGS
AF:
0.116
AC:
403
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.0
DANN
Benign
0.52

Splicing

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: rs2295890; hg19: chr6-86159462; COSMIC: COSV57629036; COSMIC: COSV57629036; API